Sectioning and quality control in microtomy

Abstract

To provide sectioning and quality control in preferable microtomy.SOLUTION: Provided is a histological system including a microtome and a vision system. The microtome progressively removes one or more slices from a tissue block, the tissue block comprising a tissue sample embedded within an embedding material. The vision system is associated with the microtome, and comprises: an illumination system for illuminating the tissue block including a tissue sample embedded within an embedding material; an imaging system for imaging the tissue block and generating imaging data to be associated with the tissue block; and a processor communicating with the imaging system, receiving the imaging data and is programmed to execute sectioning and quality control analysis.SELECTED DRAWING: Figure 1

Description

[Technical Field]

[0001] (CROSS-REFERENCE TO RELATED APPLICATIONS) This application is a division of U.S. Provisional Application No. 62 / 980,201, filed February 22, 2020; U.S. Provisional Application No. 62 / 980,203, filed February 22, 2020; U.S. Provisional Application No. 62 / 980,202 ...4, filed February 22, 2020; No. 0,194, and claims the benefit of and priority to U.S. Provisional Application No. 63 / 134,399, filed January 6, 2021, U.S. Utility Application No. 17 / 182,139, filed February 22, 2021, U.S. Utility Application No. 17 / 182,133, filed February 22, 2021, and U.S. Utility Application No. 17 / 182,166, filed February 22, 2021.

[0002] The present invention relates to quality control of cut tissue sections transferred from biological tissue sample blocks to slides, including sectioning, tracking, and mechanical quality control. In particular, this can be achieved using an automated system. [Background technology]

[0003] Traditional microtomy, the generation of postage-stamp-sized, micron-thin tissue sections for microscopic viewing, is a delicate and time-consuming manual task. In the process, a microtome cuts a tissue block consisting of a tissue sample encapsulated in a support block of embedding material, such as paraffin wax. The microtome holds a blade aligned to cut slices from one side of the tissue block, i.e., the block cut surface. A common type of rotary microtome linearly oscillates a chuck that holds the block with the cutting surface at the blade cut surface. In combination with incremental advancement of the block cut surface toward the cut surface, the microtome continuously scrapes thin tissue sections from the block cut surface. For sections with paraffin wax embedding media, the operator carefully picks up these tissue sections and floats them on warm water. The water gently smooths out wrinkles and reduces deformation from cutting. Finally, the operator transfers the sections from the water to microscope slides for further processing.

[0004] Recent advances in digital imaging of tissue sample sections have made it desirable to slice specimen blocks very quickly. For example, when tissue is sectioned as part of a clinical procedure, time is a critical variable in improving patient treatment. For example, when examining the margins of a lung cancer to determine whether sufficient tissue has been removed, every minute saved during tissue sectioning for intraoperative applications in anatomic pathology is clinically valuable. To rapidly create numerous sample sections, it would be desirable to automate the process of cutting tissue sections from a specimen block with a microtome blade and facilitate the transfer of the cut tissue sections to adhesive tape or other transport media without reducing section quality. Additionally, numerous tissue sample sections cut from the block need to be transferred to microscope slides for evaluation.

[0005] Quality control for tissue samples is important. Improper quality control can adversely affect pathology and lead to inaccurate assessment of the tissue. However, currently, quality control of tissue sections deposited on glass slides is a resource-consuming task.

[0006] This comparison is performed during manual transfer of tissue to the slide; however, it is often difficult to distinguish the tissue from the paraffin, leading to inaccurate comparisons and therefore improper quality control. Furthermore, failure to properly assess the tissue results in a lack of knowledge that an insufficient tissue section has been placed on the slide. This also prevents assessment of whether the tissue section on the slide is damaged.

[0007] The present disclosure overcomes current workflow problems and deficiencies through the implementation of methods and systems that eliminate, or at least significantly reduce, quality control issues and the risk of discrepancies between slide labels and tissue sections. Summary of the Invention [Means for solving the problem]

[0008] In some embodiments, a method for sectioning a tissue block is provided, the method comprising: imaging the tissue block to generate imaging data of the tissue block, the tissue block comprising a tissue sample embedded in a embedding material; estimating a depth profile of the tissue block based on the imaging data, the depth profile comprising a thickness of the embedding material to be removed to expose the tissue sample to a predetermined criterion; and removing the thickness of the embedding material to expose the tissue to the predetermined criterion.

[0009] In some embodiments, the method further includes progressively removing one or more sections from a tissue block comprising the tissue sample embedded within the embedding material, imaging the one or more sections to generate imaging data associated with the one or more sections, and verifying that the tissue sample has been exposed to a predetermined standard based on the imaging data. In some embodiments, the tissue block is imaged using structured light to determine a depth profile.

[0010] In some embodiments, a method for sectioning a tissue block is provided that includes the steps of progressively removing one or more sections from a tissue block comprising a tissue sample embedded within an embedding material, imaging the one or more sections removed from the tissue block to generate imaging data associated with the one or more sections, and determining, based on the imaging data, when a sufficient number of the one or more sections have been removed from the tissue block to expose the tissue sample to a predetermined criterion.

[0011] In some embodiments, the method may further include imaging the tissue block to generate baseline imaging data for the tissue sample prior to removing one or more sections. In some embodiments, the method may further include determining an expected contour, size, or shape of the tissue sample from the baseline imaging data. In some embodiments, the method may further include determining a depth profile of the buried material from the baseline imaging data and illuminating the tissue block with structured light in the UV range to remove a sufficient amount of buried material to expose the tissue sample to a predetermined standard.

[0012] In some embodiments, the method further includes comparing imaging data of a section containing the tissue sample with baseline imaging data to determine when the tissue sample is sufficiently exposed. In some embodiments, the imaging data of the section comprises imaging data of one or more sections on a tissue block, a transport medium, or a slide. In some embodiments, the contour, size, or shape of the tissue sample in the one or more sections is compared to the contour, size, or shape of the tissue sample expected from the baseline imaging data. In some embodiments, the method further includes determining a depth profile by one or more of parallax, focus, or light field imaging, and increasing the contrast between the tissue sample and the embedded material.

[0013] In some embodiments, a method for sectioning a tissue block can be provided that includes removing a thickness of embedding material from a tissue block comprising a tissue sample embedded within the embedding material, the thickness being configured to expose the tissue sample to a predetermined criterion; following the thickness removing step, progressively removing one or more sections from the tissue block; imaging the one or more sections removed from the tissue block to generate imaging data associated with the one or more sections; and confirming from the imaging data that the tissue sample has been exposed to the predetermined criterion.

[0014] In some embodiments, a histology system can be provided that includes a microtome configured to progressively remove one or more sections from a tissue block, the tissue block comprising a tissue sample embedded in an embedding material, and a vision system associated with the microtome. The vision system can include an illumination system configured to illuminate the tissue block comprising the tissue sample embedded in the embedding material, an imaging system configured to image the tissue block and generate imaging data associated with the tissue block, and a processor in communication with the vision system, the processor programmed to receive the imaging data and determine, based on the imaging data, when the tissue block has been sufficiently sectioned by the microtome.

[0015] In some embodiments, the processor is further programmed to determine when the tissue block is sufficiently sectioned by recognizing the amount of tissue sample exposed. In some embodiments, the processor is further programmed to determine an expected contour, size, or shape of the tissue sample from baseline imaging data generated by imaging the tissue block with structured light prior to removing one or more sections from the tissue block. In some embodiments, the illumination system is configured to illuminate the tissue block with structured light.

[0016] In some embodiments, the histology system may further include a transfer medium for transferring one or more sections comprising the tissue sample from the tissue block to one or more slides, and the processor is further programmed to compare the one or more sections on the tissue block, on the transfer medium, or on the one or more slides with baseline imaging data generated by imaging the tissue block with UV light prior to removing the one or more sections from the tissue block.

[0017] In some embodiments, a vision system is provided that includes an illumination system configured to illuminate a tissue block comprising a tissue sample embedded within an embedding material; an imaging system configured to image the tissue block and generate imaging data of the tissue block; and a processor in communication with the imaging system, the processor being programmed to receive the imaging data and, based on the imaging data, determine an exposure of the tissue sample to a predetermined criterion.

[0018] The present disclosure also relates to a system and method for quality control in a histology system. In some embodiments, a method is provided that includes receiving a tissue block comprising a tissue sample embedded in an embedding material, imaging the tissue block to create first imaging data of the tissue sample in a tissue section on the tissue block, removing the tissue section from the tissue block, the tissue section comprising a portion of the tissue sample, imaging the tissue section to create second imaging data of the tissue sample in the tissue section, and comparing the first imaging data with the second imaging data to confirm correspondence of the tissue sample in the first imaging data and the second imaging data based on one or more quality control parameters.

[0019] In some embodiments, if there is no correspondence between one or more quality control parameters of the tissue sample in the first imaging data and the second imaging data, the tissue section is unacceptable. In some embodiments, the one or more quality control parameters include one or more of tissue sample shape, tissue sample size, or one or more mechanical damage. In some embodiments, the method can further include transferring the tissue section to a slide using a transfer medium, and the second imaging data comprises imaging data of the tissue section on the transfer medium or imaging data of the tissue section on the slide. In some embodiments, the method can further include comparing at least two of the first imaging data, the imaging data of the tissue section on the transfer medium, or the imaging data of the tissue section on the slide.

[0020] In some embodiments, if there is no correspondence in shape or size between the tissue sample in the first imaging data and the second imaging data, the tissue section is rejected. In some embodiments, the one or more mechanical damages are selected from the group consisting of tears, shreds, blade marks, wrinkles, cracks, bubbles, insufficient tissue sample, and incomplete tissue sample. In some embodiments, the method further includes identifying the tissue section as rejected if one or more mechanical damages are present in the tissue sample in the second imaging data but not in the tissue sample in the first imaging data. In some embodiments, the method further includes adjusting one or more operating parameters associated with removing the tissue section to correct for the one or more mechanical damages. In some embodiments, the method further includes approving the tissue section if no mechanical damage is present in the tissue sample in the first imaging data and the second imaging data. In some embodiments, the method further includes rejecting the tissue block if one or more mechanical damages are present in both the first imaging data and the second imaging data.

[0021] In some embodiments, one or both of the imaging steps includes illuminating the tissue sample with UV light and imaging the tissue sample with a visible range camera to generate first imaging data or second imaging data. In some embodiments, the method further includes illuminating the tissue section to enhance contrast between the tissue sample and embedded material within the tissue sample. In some embodiments, one or both of the imaging steps includes imaging the tissue section in one or more wavelength ranges, generating imaging data of the tissue section, segmenting the tissue sample from embedded material based on color and intensity information in the color imaging data, and identifying the size, shape, or edge of the tissue sample in the tissue section.

[0022] In some embodiments, the method may further include imaging the tissue block prior to removing one or more sections to generate baseline imaging data for the tissue sample. In some embodiments, the method may further include illuminating the tissue block with UV light. In some embodiments, the method may further include comparing the first imaging data, the second imaging data, or both, with the baseline imaging data. In some embodiments, the method may further include comparing a contour, size, or shape of the tissue sample in the first imaging data, the second imaging data, or both, to an expected contour, size, or shape of the tissue sample from the baseline imaging data.

[0023] In some embodiments, a vision system is provided that includes an illumination system configured to illuminate a tissue sample, an imaging system configured to generate imaging data of the tissue section illuminated by the illumination system, and a processor in communication with the imaging system to receive the imaging data and perform one or more quality control analyses based on the imaging data. In some embodiments, the one or more quality control analyses are one or more of a comparative analysis of the tissue block and the tissue section on the slide, an analysis of mechanical properties of the tissue section, an analysis of tissue sample sufficiency, or an analysis of sample representation on the slide.

[0024] In some embodiments, a histology system is provided that may include a microtome configured to generate one or more tissue sections from a tissue block, a transport system configured to transport the one or more tissue sections from the microtome to one or more slides, and a vision system. The vision system may include an illumination system configured to illuminate the tissue sample and an imaging system configured to create imaging data of the tissue sections illuminated by the illumination system. A processor receives the imaging data and communicates with the imaging system to perform one or more quality control analyses based on the imaging data. In some embodiments, the one or more quality control analyses are one or more of a comparative analysis of at least two of the tissue sections on the tissue block, the tissue sections on the transport system, and the tissue sections on the slides, an analysis of mechanical properties of the tissue sections, an analysis of tissue sample sufficiency, or an analysis of sample representation on the slides.

[0025] The present disclosure also relates to systems and methods for tracking and printing within a histology system. In some embodiments, a system is provided that includes an information reader configured to read identification data associated with a tissue block, a microtome configured to cut one or more tissue sections from the tissue block, one or more slides for receiving the one or more tissue sections, and a printer configured to receive the identification data and print one or more indicia for the one or more slides after the one or more tissue sections have been cut from the tissue block, the one or more indicia comprising information associating the one or more tissue sections on the one or more slides with the tissue block.

[0026] In some embodiments, the system may further include a transfer medium configured to transfer one or more tissue sections from the microtome to one or more slides. In some embodiments, the transfer medium includes markings indicative of identification data for the one or more tissue sections, the markings configured to associate the one or more tissue sections with the tissue block. In some embodiments, the system may further include a transfer medium marking device for marking the transfer medium with markings indicative of identification data for the one or more tissue sections, the markings configured to associate the one or more tissue sections with the tissue block.

[0027] In some embodiments, the system may further include a visualization system configured to track one or more tissue sections from the microtome to one or more slides. In some embodiments, the visualization system is configured to perform a comparison between one or more tissue sections on the one or more slides and one or more images of the tissue block or images of the sections on the transport medium. In some embodiments, the visualization system is configured to perform a comparison between one or more tissue sections on the one or more slides, tissue block, or transport medium and a baseline image of the tissue sample in the tissue block generated by imaging the tissue block with UV light prior to removing the one or more sections from the tissue block. For example, the comparison is based on the size, shape, and contour of the tissue sample in the one or more tissue sections. In some embodiments, the visualization system is configured to read one or more labels on the slide and confirm their association with identification data for the sample block. In some embodiments, the printer prints labels individually for one or more samples.

[0028] In some embodiments, a system can be provided that includes an information reader configured to read identification data from a tissue block, a microtome configured to cut one or more tissue sections from the tissue block, a transport medium configured to transfer the one or more tissue sections to one or more slides, and a printer. A processor is configured to receive the identification data and cause the microtome to cut the one or more tissue sections and subsequently cause the printer to print one or more indicia for the one or more slides, where the one or more indicia can comprise information associating the one or more tissue sections on the one or more slides with the tissue block.

[0029] In some embodiments, the transfer medium includes markings indicating identification data for the one or more tissue sections, the markings configured to associate the one or more tissue sections with the tissue block. In some embodiments, the system further includes a transfer medium marking device for marking the transfer medium with markings indicating identification data for the one or more tissue sections, the markings can be configured to associate the one or more tissue sections with the tissue block. In some embodiments, the system further includes a visualization system configured to track the one or more tissue sections from the microtome to the one or more slides. In some embodiments, the visualization system is configured to perform a comparison between the one or more tissue sections on the one or more slides and the one or more sections on the tissue block. For example, the comparison is based on the size and margins of the tissue in the one or more tissue sections.

[0030] In some embodiments, a method is provided for tracking samples in microtomy, comprising the steps of reading identification data from a tissue block; cutting a first set of one or more tissue sections from the tissue block; and following cutting, printing one or more labels for one or more slides, wherein the one or more labels comprise information associating the one or more tissue sections on the one or more slides with the tissue block; and transferring the one or more tissue sections to one or more slides and labeling the one or more slides with the one or more labels.

[0031] In some embodiments, the method further includes comparing the one or more tissue sections on the slides with the one or more tissue sections on the block to confirm association of the one or more tissue sections on the one or more slides with the tissue block. In some embodiments, the method further includes cutting a second set of one or more tissue sections only after the first set of one or more tissue sections have been placed on the one or more slides and labeled with one or more labels. In some embodiments, the method further includes comparing the one or more tissue sections on the one or more slides to a baseline image of the tissue sample in the tissue block generated by imaging the tissue block with UV light prior to removing the one or more sections from the tissue block. The present specification also provides, for example, the following items: (Item 1) 1. A method for sectioning a tissue block, comprising: imaging a tissue block and generating imaging data of the tissue block, the tissue block comprising a tissue sample embedded in an embedding material; estimating a depth profile of the tissue block based on the imaging data, the depth profile comprising a thickness of the buried material to be removed to expose the tissue sample to a predetermined standard; removing a thickness of said embedding material to expose said tissue sample to said predetermined criteria; A method comprising: (Item 2) progressively removing one or more sections from a tissue block comprising a tissue sample embedded within an embedding material; imaging the one or more slices and generating imaging data associated with the one or more slices; determining, based on the imaging data, that the tissue sample has been exposed to the predetermined standard; Item 1, the method of claim 1 further comprising: (Item 3) 2. The method of claim 1, wherein the tissue block is imaged using structured light to determine the depth profile. (Item 4) 1. A method for sectioning a tissue block, comprising: progressively removing one or more sections from a tissue block comprising a tissue sample embedded within an embedding material; imaging the one or more sections removed from the tissue block to generate imaging data associated with the one or more sections; determining, based on the imaging data, when a sufficient number of the one or more sections have been removed from the tissue block to expose the tissue sample to a predetermined standard; A method comprising: (Item 5) 5. The method of claim 4, further comprising imaging the tissue block prior to removing the one or more sections to generate baseline imaging data for the tissue sample. (Item 6) 6. The method of claim 5, further comprising determining an expected contour, size, or shape of the tissue sample from the baseline imaging data. (Item 7) 6. The method of claim 5, further comprising determining a depth profile of the buried material from the baseline imaging data to remove a sufficient amount of the buried material to expose the tissue sample to the predetermined criteria. (Item 8) 6. The method of claim 5, further comprising illuminating the tissue block with structured light in the UV range. (Item 9) 6. The method of claim 5, further comprising comparing imaging data of the section containing the tissue sample with the baseline imaging data to determine when the tissue sample has been sufficiently exposed. (Item 10) 10. The method of claim 9, wherein the imaging data of the section comprises imaging data of the one or more sections on the tissue block, on a transport medium, or on a slide. (Item 11) 10. The method of claim 9, wherein the contour, size, or shape of the tissue sample in the one or more sections is compared to the contour, size, or shape of the tissue sample expected from the baseline imaging data. (Item 12) Item 5. The method of item 4, further comprising determining a depth profile by one or more of parallax, focus, or light field imaging. (Item 13) 5. The method of claim 4, further comprising increasing the contrast between the tissue sample and the embedding material. (Item 14) 1. A method for sectioning a tissue block, comprising: removing a thickness of embedding material from a tissue block comprising a tissue sample embedded within the embedding material, the thickness of the embedding material being configured to expose the tissue sample to a predetermined standard; following the thickness removal step, progressively removing one or more sections from the tissue block; imaging the one or more sections removed from the tissue block to generate imaging data associated with the one or more sections; determining from the imaging data that the tissue sample has been exposed to the predetermined standard; A method comprising: (Item 15) 1. A histology system comprising: a microtome configured to progressively remove one or more sections from a tissue block, the tissue block comprising a tissue sample embedded within an embedding material; a vision system associated with the microtome, an illumination system configured to illuminate the tissue block comprising a tissue sample embedded in an embedding material; an imaging system configured to image the tissue block and generate imaging data associated with the tissue block; a processor in communication with the vision system, the processor receiving the imaging data and determining based on the imaging data whether the tissue block is to be microtomed by the microtome; a processor programmed to determine when the tissue has been sufficiently sectioned by a vision system comprising: A histology system comprising: (Item 16) 16. The histology system of claim 15, wherein the processor is further programmed to determine when the tissue block has been sufficiently sectioned by recognizing the amount of tissue sample exposed. (Item 17) 16. The histology system of claim 15, wherein the processor is further programmed to determine an expected contour, size, or shape of the tissue sample from baseline imaging data generated by imaging the tissue block with structured light prior to removing the one or more sections from the tissue block. (Item 18) 16. The histology system of claim 15, wherein the illumination system is configured to illuminate the tissue block with structured light. (Item 19) 18. The histology system of claim 17, further comprising a transfer medium for transferring one or more sections comprising a tissue sample from the tissue block to one or more slides, wherein the processor is further programmed to compare the one or more sections on the tissue block, on the transfer medium, or on the one or more slides with baseline imaging data generated by imaging the tissue block with UV light prior to removing the one or more sections from the tissue block. (Item 20) 1. A vision system comprising: an illumination system configured to illuminate a tissue block comprising a tissue sample embedded within an embedding material; an imaging system configured to image the tissue block and generate imaging data of the tissue block; a processor in communication with the imaging system, the processor being programmed to receive the imaging data and determine an exposure of the tissue sample to a predetermined criterion based on the imaging data; A vision system comprising: (Item 21) 1. A method for quality control in a histology system, comprising: receiving a tissue block comprising a tissue sample embedded in an embedding material; imaging the tissue block to generate first imaging data of the tissue sample in a tissue section on the tissue block; removing the tissue section from the tissue block, the tissue section comprising a portion of the tissue sample; imaging the tissue section and generating second imaging data of the tissue sample in the tissue section; comparing the first imaging data with the second imaging data and confirming a correspondence of the tissue samples in the first imaging data and the second imaging data based on one or more quality control parameters; A method comprising: (Item 22) 22. The method of claim 21, wherein if there is no correspondence of one or more quality control parameters in the tissue sample in the first imaging data and the second imaging data, the tissue section is unqualified. (Item 23) 23. The method of claim 22, wherein the one or more quality control parameters comprise one or more of the shape of the tissue sample, the size of the tissue sample, or one or more mechanical damages. (Item 24) 22. The method of claim 21, further comprising transferring the tissue section to a slide using a transfer medium, wherein the second imaging data comprises imaging data of the tissue section on the transfer medium or imaging data of the tissue section on the slide. (Item 25) 25. The method of claim 24, further comprising comparing at least two of the first imaging data, the imaging data of the tissue section on the transport medium, or the imaging data of the tissue section on the slide. (Item 26) 24. The method of claim 23, wherein if there is no correspondence in shape or size of the tissue sample in the first imaging data and the second imaging data, the tissue section is unqualified. (Item 27) 24. The method of claim 23, wherein the one or more mechanical damages are selected from the group consisting of tears, shreds, blade marks, wrinkles, cracks, bubbles, insufficient tissue sample, and incomplete tissue sample. 1. The method of claim 27, further comprising identifying a tissue section as unqualified if one or more mechanical damages are present in the tissue sample in the second imaging data but not in the tissue sample in the first imaging data. (Item 28) 30. The method of claim 28, further comprising adjusting one or more operating parameters associated with the removal of the tissue section to compensate for one or more mechanical damages. (Item 29) 29. The method of claim 28, further comprising the step of approving the tissue section if no mechanical damage is present in the tissue sample in the first imaging data and the second imaging data. (Item 30) 29. The method of claim 28, further comprising rejecting the tissue block if one or more mechanical damages are present in both the first imaging data and the second imaging data. (Item 31) 22. The method of claim 21, wherein one or both of the imaging steps includes illuminating the tissue sample with UV light and imaging the tissue sample with a visible range camera to generate the first imaging data or the second imaging data. (Item 32) 22. The method of claim 21, further comprising illuminating the tissue section to enhance contrast between the tissue sample and the embedded material within the tissue sample. (Item 33) One or both of the imaging steps may include: imaging the tissue section in one or more wavelength ranges; generating imaging data of the tissue slice; segmenting the tissue sample from the embedded material based on color and intensity information in the color imaging data; identifying the size, shape, or edge of the tissue sample in the tissue section; 22. The method according to item 21, comprising: (Item 34) 22. The method of claim 21, further comprising imaging the tissue block prior to removing the one or more sections to generate baseline imaging data for the tissue sample. (Item 35) 35. The method of claim 34, further comprising illuminating the tissue block with UV light. (Item 36) 35. The method of claim 34, further comprising comparing the first imaging data, the second imaging data, or both, to the baseline imaging data. (Item 37) 35. The method of claim 34, further comprising comparing a contour, size, or shape of the tissue sample in the first imaging data, the second imaging data, or both, with an expected contour, size, or shape of the tissue sample from the baseline imaging data. (Item 38) 1. A vision system comprising: an illumination system configured to illuminate the tissue section; an imaging system configured to generate imaging data of the tissue section illuminated by the illumination system; a processor in communication with the imaging system to receive the imaging data and perform one or more quality control analyses based on the imaging data; A vision system comprising: (Item 39) Item 39. The vision system of item 38, wherein the one or more quality control analyses are one or more of a comparative analysis of a tissue block and the tissue section on a slide, an analysis of mechanical properties of the tissue section, an analysis of the sufficiency of the tissue sample, or an analysis of sample representation on a slide. (Item 40) 1. A histology system comprising: a microtome configured to generate one or more tissue sections from the tissue block; a transfer system configured to transfer the one or more tissue sections from the microtome to one or more slides; 1. A vision system comprising: an illumination system configured to illuminate the tissue sample; an imaging system configured to generate imaging data of the tissue section illuminated by the illumination system; a vision system comprising: a processor in communication with the imaging system to receive the imaging data and perform one or more quality control analyses based on the imaging data; A histology system comprising: (Item 41) 41. The histology system of claim 40, wherein the one or more quality control analyses are one or more of a comparative analysis of at least two of the tissue section on a tissue block, the tissue section on the transport system, and the tissue section on a slide, an analysis of mechanical properties of the tissue section, an analysis of tissue sample sufficiency, or an analysis of sample representation on a slide. (Item 42) 1. A system comprising: an information reader configured to read identification data associated with the tissue block; a microtome configured to cut one or more tissue sections from the tissue block; one or more slides for receiving said one or more tissue sections; a printer configured to receive the identification data and print one or more indicia for the one or more slides after the one or more tissue sections have been cut from the tissue block, the one or more indicia comprising information associating the one or more tissue sections on the one or more slides with the tissue block; and A system comprising: (Item 43) 43. The system of claim 42, further comprising a transport medium configured to transport the one or more tissue sections from the microtome to the one or more slides. (Item 44) Item 44. The system of item 43, wherein the transport medium includes markings indicating the identification data for the one or more tissue sections, the markings configured to associate the one or more tissue sections with the tissue block. (Item 45) Item 44. The system of item 43, further comprising a transfer medium marking device for marking the transfer medium with markings indicative of the identification data relating to the one or more tissue sections, the markings configured to associate the one or more tissue sections with the tissue block. (Item 46) Item 43. The system of item 42, further comprising a visualization system configured to track the one or more tissue sections from the microtome to the one or more slides. (Item 47) Item 47. The system of item 46, wherein the visualization system is configured to perform a comparison between the one or more tissue sections on the one or more slides and one or more images of the tissue block or images of the sections on a transport medium. (Item 48) Item 48. The system of item 47, wherein the visualization system is configured to perform a comparison between the one or more tissue sections on the one or more slides, the tissue block, or the transport medium and a baseline image of the tissue sample in the tissue block generated by imaging the tissue block with UV light prior to removing the one or more sections from the tissue block. (Item 49) Item 49. The system of item 48, wherein the comparison is based on the size, shape, and contour of the tissue sample in the one or more tissue sections. (Item 50) Item 47. The system of item 46, wherein the visualization system is configured to read the one or more labels on the slide and verify their association with the identification data for the sample block. (Item 51) Item 43. The system of item 42, wherein the printer prints the indicia individually for the one or more samples. (Item 52) 1. A system comprising: an information reader configured to read identification data from the tissue block; a microtome configured to cut one or more tissue sections from the tissue block; a transfer medium configured to transfer the one or more tissue sections to one or more slides; A printer and a processor configured to receive the identification data, cause the microtome to cut the one or more tissue sections, and subsequently cause the printer to print one or more indicia for the one or more slides, the one or more indicia comprising information associating the one or more tissue sections on the one or more slides with the tissue block; A system comprising: (Item 53) Item 54. The system of item 53, wherein the transport medium includes markings indicating the identification data regarding the one or more tissue sections, the markings configured to associate the one or more tissue sections with the tissue block. (Item 54) Item 54. The system of item 53, further comprising a transfer medium marking device for marking the transfer medium with markings indicative of the identification data relating to the one or more tissue sections, the markings configured to associate the one or more tissue sections with the tissue block. (Item 55) Item 54. The system of item 53, further comprising a visualization system configured to track the one or more tissue sections from the microtome to the one or more slides. (Item 56) Item 54. The system of item 53, further comprising a visualization system configured to perform a comparison between the one or more tissue sections on the one or more slides and the one or more sections on the tissue block. (Item 57) 57. The system of claim 56, wherein the comparison is based on the size and margins of tissue in the one or more tissue sections. (Item 58) 1. A method for tracking a sample in a microtomy, the method comprising: reading identification data from the tissue block; cutting a first set of one or more tissue sections from the tissue block; printing one or more indicia on one or more slides following cutting, the one or more indicia comprising information associating the one or more tissue sections on the one or more slides with the tissue block; transferring the one or more tissue sections to one or more slides and labeling the one or more slides with the one or more labels; A method comprising: (Item 59) comparing the one or more tissue sections on the slide with the one or more tissue sections on the block to confirm an association of the one or more tissue sections on the one or more slides with the tissue block. Item 59. The method according to Item 58, comprising: (Item 60) 59. The method of claim 58, further comprising cutting a second set of one or more tissue sections only after the first set of one or more tissue sections have been mounted on the one or more slides and labeled with the one or more labels. (Item 61) 59. The method of claim 58, further comprising comparing the one or more tissue sections on the one or more slides to a baseline image of the tissue sample in the tissue block generated by imaging the tissue block with UV light prior to removing the one or more sections from the tissue block. [Brief explanation of the drawings]

[0032] So that those skilled in the art to which the subject invention pertains will more readily understand how to make and use the surgical devices and systems disclosed herein, preferred embodiments thereof will be described in detail hereinafter with reference to the drawings.

[0033] [Figure 1] FIG. 1 illustrates an exemplary system for performing quality control analysis of a histology system.

[0034] [Figure 2] FIG. 2 illustrates one embodiment of an illumination and imaging system for increasing tissue contrast relative to paraffin.

[0035] [Figure 3] FIG. 3 illustrates an exemplary tissue block showing the tissue inside the embedded material.

[0036] [Figure 4] 4A, 4B, 4C, 4D, 4E, and 4F illustrate the progression of images from an unprocessed block to a fully sectioned block.

[0037] [Figure 5] FIG. 5 is an exemplary flowchart illustrating a method for comparing an image of a tissue section with a baseline image of a tissue block.

[0038] [Figure 6] FIG. 6 is a flow chart illustrating a method for making a sectioning decision.

[0039] [Figure 7] Figures 7 and 8 are images of tissue ribbons under UV illumination. [Figure 8] Figures 7 and 8 are images of tissue ribbons under UV illumination.

[0040] [Figure 9] FIG. 9 is a flow chart illustrating a method for making cross-sectioning determinations in which the cut ribbon and block face are imaged.

[0041] [Figure 10] FIG. 10 is a flow chart illustrating various methods for block sectioning.

[0042] [Figure 11] 11A and 11B illustrate example images of tissue embedded within an embedding material and associated example graphs showing the relationship between the tissue and the embedding material.

[0043] [Figure 12] 12A and 12B illustrate example images of tissue embedded within an embedding material and associated example graphs showing the relationship between the tissue and the embedding material.

[0044] [Figure 13] FIG. 13 illustrates an example image related to laser dot diffusion.

[0045] [Figure 14]FIG. 14 illustrates an exemplary graph relating column 2 dots sampled at 1 pixel across a block of laser dots on a tissue block.

[0046] [Figure 15] FIG. 15 illustrates an example image showing the micro-serrations that the blade can leave on the tissue block.

[0047] [Figure 16] FIG. 16 illustrates an exemplary system for performing tissue comparison and mechanical quality control analysis of a histology system.

[0048] [Figure 17A] FIG. 17A is a section comparison of a sample block and a tissue section on a glass slide.

[0049] [Figure 17B] Figure 17B is a slide and paraffin block discrimination comparison.

[0050] [Figure 18] 18 and 19 are exemplary images of tissue ribbons under UV illumination. [Figure 19] 18 and 19 are exemplary images of tissue ribbons under UV illumination.

[0051] [Figure 20] FIG. 20 is a flow chart illustrating how the cut section and block face are imaged.

[0052] [Figure 21A]FIG. 21A is a schematic diagram of one embodiment of the automated tape transport device of the present disclosure illustrating the tape path, the device having a barcode reader to scan the markings on the sample block and the printed glass slides in accordance with the just-in-time printing, tracking, and identification of cut tissue sections of the present disclosure, a tape marking or printing device laser etches or prints identification marks on the tape transport medium, and the glass slides are printed in real time by a separate slide printer.

[0053] [Figure 21B] FIG. 21B is a schematic diagram of one embodiment of an automated tape transport device of the present disclosure illustrating the path of an optionally pre-printed tape, the device having a barcode reader to scan the markings on the sample block and the printed glass slides, which are printed in real time by a separate slide printer, in accordance with the tracking and identification of cut tissue sections of the present disclosure.

[0054] [Figure 22] FIG. 22 is a flow chart illustrating one embodiment of the automated steps of the system, which has a barcode scanning, tape media marking, and slide printing system to enable tracking of tissue sections from block to tape to glass slide.

[0055] [Figure 23] FIG. 23 is a workflow diagram of the section tracking system.

[0056] [Figure 24] FIG. 24 illustrates an exemplary embodiment of an automated microtomy device.

[0057] [Figure 25] FIG. 25 is a schematic diagram of an exemplary embodiment of an automated tape transport apparatus illustrating the path of the tape, the apparatus having an imaging device for taking images of the sample block and slides.

[0058] [Figure 26] 26 is a perspective view of a slide station of the automated apparatus of FIG. 6. FIG.

[0059] ;

[0060] [Figure 27] FIG. 27 is a schematic diagram showing the tape prior to being applied to the face of the sample block.

[0061] [Figure 28A] FIG. 28A is an elevational view illustration of a sample system layout, according to some embodiments of the present disclosure.

[0062] [Figure 28B] 28B and 28C are isometric illustrations of a sample system layout, according to some embodiments of the present disclosure. [Figure 28C] 28B and 28C are isometric illustrations of a sample system layout, according to some embodiments of the present disclosure.

[0063] [Figure 29] FIG. 29 is a flowchart illustrating the processing of a tissue block in an automated tissue sectioning system, according to some embodiments of the present disclosure.

[0064] [Figure 30] FIG. 30 is a flow chart illustrating the automated steps of the system of FIG.

[0065] [Figure 31] FIG. 31 is a flow chart illustrating one embodiment of the automated steps of the present system having an imaging device to determine whether a tissue section is sufficient for transfer to a slide.

[0066] [Figure 32]FIG. 32 is a flow chart illustrating the automated steps of an alternative embodiment of the present device.

[0067] [Figure 33] FIG. 33 is a flow chart illustrating the automated steps of an alternative embodiment of the present device.

[0068] [Figure 34] FIG. 34 is an exemplary embodiment of a computing device. DETAILED DESCRIPTION OF THE INVENTION

[0069] Detailed Description The present disclosure provides systems and methods for various quality control analyses on tissue samples during microtomy. An exemplary embodiment of a system and method for quality control of tissue samples is shown in FIG. 1. Such a system can be configured to provide various types / aspects of quality control 100, including printing and tracking 102, tissue sectioning analysis 104, and mechanical tissue integrity analysis 106.

[0070] As shown, tissue sections can be cut from a tissue sample, such as a sample block. Various quality control analyses can be performed in connection with the tissue section to determine the integrity of the tissue section. As will be explained in more detail below, one or more analyses can be performed as the tissue section is being transferred from the sample block to a slide or other medium, or can be performed once the tissue section is on a slide or other medium. The process can be performed manually or using an automated system.

[0071] To perform various quality control analyses, various images of the tissue block and tissue section can be taken for comparison. For example, images can be taken including, but not limited to, images before tissue sectioning to create a baseline image of the block, the surface of the tissue block, the tissue section after it has been cut from the tissue block, the tissue section as it is being transported via a transport system or tape, and the tissue section positioned on a slide. Comparison of any of these images can be used to determine whether the tissue section is satisfactory once positioned on the slide. If the comparison reveals any problems or errors, depending on the type of problem or error identified, the tissue slice can be discarded, the tissue block can be discarded, and / or adjustments can be made to any of the physical components of the system. Various operating parameters can be adjusted based on the type of mechanical damage or defect detected using the vision system of the present disclosure. Such operating parameters include, but are not limited to, sharpening or replacing the microtome blade, adjusting the hydration time or temperature, replacing the transport medium, or adjusting the operating parameters (e.g., speed) of the transport medium or the pressure applied to the transport medium against the tissue section.

[0072] In some embodiments, an analysis is performed that compares the tissue section to the sample block to match the tissue section to the sample block. In some embodiments, an analysis is performed to determine the condition of the tissue section either during transport or after slide placement. Additional analyses of the tissue section can be performed, as will be discussed in more detail below. Furthermore, various methods can be used to perform quality control, including, but not limited to, the use of a visualization / imaging system that can be configured to image one or more of the tissue sample block, the tissue section during transport, and the tissue section on the slide, so that the images can be used to perform one or more of the quality control analyses.

[0073] In some embodiments, the histology system can provide tracking and comparative analysis of cut tissue sections in manual or automated tissue transfer devices / systems. The determination system analyzes / compares one or more parameters or properties / characteristics of the cut tissue sections on the microscope slide and the sample block. Alternatively, or in addition, the system analyzes / compares one or more parameters or properties / characteristics of the cut tissue sections on the microscope slide and the cut tissue sections (slices) immediately after they are cut from the sample block. These systems ensure that the sections on the glass slides are properly matched to the tissue sample block. This is the comparative aspect of a quality control system that improves sample tracking in the laboratory.

[0074] In some embodiments, a system is provided that can provide feedback to allow for self-correction or adaptation. This feedback system provides another aspect of quality control.

[0075] In some embodiments, the system also provides a quality control feedback system. In some embodiments, for example, once the quality control system sends a flag, a feedback process can be triggered, resulting in various actions being taken automatically without human intervention. For example, if a flag, e.g., a discrepancy, is present, examples of downstream actions that can be taken include issuing instructions or recalibrating an algorithm, thus allowing the system / process to self-correct or adapt. In some embodiments, the feedback process can interact with block sectioning decisions. In the quality control process, when a defect is detected, the root cause is searched for to resolve the problem. Thus, when a defect is detected by the quality control process, a predetermined set of possible root causes will be checked. For example, if there is an air bubble under the tissue section on the glass, this may mean that the transport medium (tape) to the glass applicator roller is faulty, and the user can be warned about this. Or, if the tissue is being sectioned in the automated QC image, the system will force a new sectioning blade change in the microtome. Once the root cause is identified, one or more operating parameters can be altered as described above.

[0076] For example, in an exemplary embodiment of a feedback system, the QC system suddenly one day begins generating an increased number of flags regarding section quality. This can indicate that conditions in the system have changed and corrective action is required. The increased discrepancy rate can trigger a set of self-tests, one of which may then trigger a corrective mechanism (e.g., replacing the microtome blade). As another example, suppose it is noted that tissue begins to run off the slide at a high rate. This could mean that the sectioning algorithm is failing or that the tissue is detaching from the tape; again, a self-test could trigger corrective action. It should be understood that these are provided merely as examples, as other actions in response to various events are also contemplated in a quality control feedback system.

[0077] It should be understood that the feedback loop may be used in conjunction with the other quality systems disclosed herein.

[0078] It should be understood that any transport medium (also referred to as a transport medium) other than tape may be utilized, and thus references to tape herein are used for convenience, as the systems and methods disclosed herein are fully applicable to other transport media than just tape.

[0079] Sample preparation

[0080] The sample may be a tissue, organ, organism, frozen liquid, or other biological sample. In some embodiments, the sample may be pre-stained or pre-treated in some other manner to facilitate sectioning, as will be discussed in more detail below. The process of initial sample preparation, in some embodiments, may include: a) transferring the biological tissue into a container of fixative, such as formalin, upon removal from the organism; b) transferring the tissue after fixation into a labeled tissue cassette; and c) after transfer to the cassette, processing the tissue by: i) dehydrating via immersion in alcohol to remove water and formalin; ii) purging via solvent to remove alcohol; and iii) applying an embedding material, such as paraffin wax, to surround the tissue within a large block of molten material and create a "sample block." Paraffin is poured over the dried, chemically treated tissue within a mold. In some cases, the histotechnician compresses the tissue during the molding process, but paraffin is always present between the bottom of the mold and the tissue sample. Once the block solidifies, it provides a support matrix during the tissue sectioning process. Once the paraffin has cooled, it is removed from the mold, forming a paraffin block into which the tissue is embedded. The molded tissue-paraffin combination is supported on a plastic cassette, which provides the tissue-holding feature for the microtome clamp. On the other side of the cassette, the paraffin / tissue combination is cantilevered. This side corresponds to the bottom of the mold in the previous step. Excess paraffin resulting from molding must be removed to expose the tissue so that tissue sections can be identified and analyzed / evaluated. The thickness of the excess paraffin can vary greatly, from tens to hundreds of microns.

[0081] The plastic cassettes holding the tissues in the paraffin molds can have different colors. In some embodiments, the quality control system detects the color of the cassettes holding the sample blocks to cross-check the sample type. In some laboratories, the laboratory assigns these colors to certain tissue types. For example, a laboratory may choose to use pink cassettes for breast tissue. If the system detects a color that is significant to the laboratory, it can cross-check the sample type with the laboratory data to ensure that the colors match. This provides an additional backup for the quality control system. This data can also be used during image processing so that variations in the image background can be effectively filtered out.

[0082] When a tissue block is placed in the chuck for sectioning, the paraffin side faces the microtome's cutting blade, but the molding process is not complete; the tissue is underneath the paraffin layer, not on top of the paraffin. A new block first undergoes sectioning, involving relatively thick sections, by removing a 0.1-1 mm layer of paraffin wax above the tissue sample. After removal of the top paraffin layer, the full contours of the tissue sample are exposed and the block is ready to be sectioned. Once the top paraffin layer is removed, tissue is typically sectioned to a thickness of 3-5 μm in clinical and research settings. This process of removing the paraffin layer and exposing a large cross-section of the tissue is referred to as block sectioning. After removal of the top paraffin layer, the tissue sample is exposed and ready to be sectioned, and then placed on tape for transfer to glass slides for analysis, e.g., pathology or histology. That is, once sufficient paraffin has been removed (the block is said to be "sectioned"), subsequent block sectioning provides tissue sections for placement onto glass slides for analysis (which are further processed for evaluation).

[0083] It should be noted that although paraffin is described herein as the embedding material, it should be understood that other embedding materials, including frozen sections, may also be utilized.

[0084] visualization system

[0085] The histology system includes a visualization system, which in some embodiments may include an illumination system and an imaging system. The illumination system assists in imaging / discriminating / differentiating tissue and paraffin, which can then be imaged by the imaging system for evaluation. Thus, differentiation of tissue from paraffin is enhanced with respect to images captured on sample blocks, tapes, and / or slides. Various illumination and imaging systems are discussed below. In some embodiments, the visualization system utilizes appropriate optics (illumination system / method, imaging system / method, detection system / method), followed by a computational process. This computational process provides a comparative assessment of images for quality control, as will be described in more detail below.

[0086] It should be understood that the term "image" includes data in any form or format generated by an imaging system that represents the image or that can otherwise be analyzed to determine information about the object being imaged. Images captured by a visualization system can be used such that the image itself can be processed, analyzed, and / or compared for quality control analysis, or any data representing the image or the object being imaged can be used, including data to create the image or data representing the image or the object being imaged.

[0087] In some embodiments, the visualization system can be configured to a) take images of i) a tissue sample block containing tissue embedded within an embedding material, ii) the block face of the tissue sample block, iii) the tissue section after it has been cut from the sample block, iv) the transport medium carrying the cut tissue section, or v) the slide containing the cut tissue section, and b) take images of the cut section from the sample block on either the slide or the transport medium (e.g., tape). In some embodiments, this can be done to enhance the image taken by the imaging device, to enhance differentiation of the tissue from the embedding material in which it is embedded.

[0088] FIG. 2 illustrates an embodiment of a visualization system 110 including an illumination system 112 and an imaging system 114 that can be used to image one or more of a tissue block, a tissue section associated with a transport system, and a tissue section associated with a slide. As shown, the illumination system 112 illuminates a sample block 116 supported on a sample support chuck 118. Note that reference numeral 122 illustrates the sample block under high-contrast illumination, where the contrast between the paraffin and the tissue is pronounced, while reference numeral 120 illustrates the sample block under low-contrast illumination, where it is more difficult to distinguish between the tissue and the paraffin. Alternatively, or in addition, the illumination can illuminate the tissue section after it has been cut from the block. Various types of illumination systems are described below. An imaging device, e.g., a camera, captures an image of the sample block 116 for evaluation. Classical image processing techniques, as described below, can be utilized for evaluation. Modern artificial intelligence based image processing techniques can also be utilized, with the teaching and testing phases all taking place at the development site.

[0089] As shown, the imaging system 114, e.g., a camera, images the block face of the sample block 116 as the illumination system 112 illuminates the block face so that tissue-to-paraffin contrast is increased. In some embodiments, the imaging system can be triggered by software or hardware to capture successive images of the block 116 as it is sectioned, which is performed without human intervention. Edge detection (finding object boundaries within an image by detecting discontinuities in brightness), color, hue, or intensity tracking in successive images, or classical image processing techniques based on similar attributes of each pixel and their variation in the context of the image, can be utilized. The imaging system can be part of an automated sectioning system, which has the ability to synchronize imaging with block sectioning, whether through software operation or a hardware trigger such as a position-sensitive switch. As noted above, images of the cut tissue section after microtome sectioning can alternatively or additionally be captured.

[0090] In some embodiments, line scanning is utilized. Line scanning involves constructing an image one line at a time using a line sensor that passes in a linear motion across an object. Thus, in this method, the area of ​​the block-tissue ribbon interface at the blade during cutting is scanned after the tissue block is cut by the blade. Software then stitches the lines together to create an image of the cut section. The line of section directly above the blade can be imaged, and a 2D image can be constructed from the series of line images. In some embodiments, the line imaging device can be mounted inside the roller for line scanning as the tape moves past the roller or as the roller moves along the tape. In some embodiments, the imaging device can be mounted outside the roller. In either case, imaging can be coupled to tape transport with transmitted light on one side of the tape. The illumination device can be inside or outside the roller. Some advantages of line scanning compared to taking a 2D image of an already cut tissue section include: i) the reconstructed line scan image will be a "flat" representation of the tissue surface and will not have the risk of wrinkles or curls, ii) it is easy to determine the boundaries of the beginning and end of the section, and iii) all parts of the image will be in focus because the blade and cutting force provide a consistent location for the tissue section.

[0091] The system can utilize one-dimensional scanning across a sample, profile, or image, all at various degrees of sampling resolution.

[0092] Imaging tissue sections on slides can also provide downstream uses for digital pathology. When scanning tissue in a slide scanning device and computationally processing it, it is beneficial to first determine (geometrically) the location within the slide where the tissue sits. This is useful for autofocus algorithms in the scanning device or to reduce computational steps in computer-aided diagnosis where the tissue is segmented. The systems described herein, for example, UV illumination fluorescence mode, provide clear visibility to enable easy segmentation. Such segmentation / location information can be passed back to a laboratory information system for downstream integration with the scanning device or computer-aided diagnosis platform when the slide with the tissue section is used.

[0093] In some embodiments, illumination and signal capture using Raman spectroscopy can be used to identify the paraffin matrix throughout the tissue. Raman spectroscopy can be used to determine vibrational, rotational, or other low-frequency modes of molecules, providing a structural guide for molecular identification. When light excites a molecule, the molecule reflects light at different wavelengths, thereby enabling the detection of the composition. That is, Raman spectroscopy quantitatively detects a substance based on scattered light. The tissue itself is impregnated with paraffin, but its density is lower than that of paraffin in other areas of the block. Progressive image capture using Raman spectroscopy of the block after each section provides a quantified metric that can be used for comparison. This method can be used in parallel with visible light imaging to a priori determine tissue area, increasing the efficiency of the implemented method.

[0094] In some embodiments, the imaging system includes a sensor and a radiation system. The method / system captures signals from the paraffin portion of a tissue block or cut section such that the level of the signal decreases as the paraffin across the tissue becomes thinner. This is due to the fact that different materials absorb different radiation wavelengths, and tissue and paraffin radiation absorption wavelengths are different. As the paraffin layer across the embedded tissue is removed, the absorption spectrum (e.g., IR absorption spectrum) will change. By tracking this change across successive images, the absorption level correlates with the amount of paraffin across the embedded tissue. In this way, the amount (or removal) of paraffin can be determined by a comparison or calculation process.

[0095] For tissue on a tape or slide, either reflection or transmission mode may be used. It may be advantageous to utilize transmission mode in terms of the location of the light source and camera. In particular, imaging of sections on tape can be performed using either a light source or a line camera by embedding the light source or camera inside a transparent roller (or a roller with a transparent window).

[0096] The illumination system can emit light, for example, in the UV, near-IR, IR, or visible / broadband ranges. The emitted light can have different colors. In some embodiments, the illumination system can include an LED, OLED, laser, light bulb, or similar light-emitting device or material. Also, as shown, the imaging system can include various areas for capturing images, including on a tissue block or tape or glass slide. A computational system processes the images, for example, quantitatively, for identification and tracking.

[0097] It should be understood that these various illumination and imaging systems and various associated methodologies described herein are provided as examples, as other illumination systems may be utilized to enhance differentiation between tissue and paraffin (or other embedding material), other imaging systems may be utilized, and other calculation or comparison processing systems may be utilized for identification tracking and sample integrity checks. Also, any combination of illumination systems and / or any combination of imaging systems may be utilized.

[0098] Light (coherent or non-coherent) can be used via absorption, refraction, scattering, Raman scattering, fluorescence, phosphorescence, interference, and wavelengths can be continuous or discontinuous anywhere in the spectrum from x-ray to radio wave, or any combination of these modalities. Reflectance modes of transmission can be utilized.

[0099] In some embodiments, the imaging system can include multiple imaging devices for imaging the sample block for quality control as described herein. The imaging devices can work together to create a single 3D image of the sample block. Various types of imaging devices can be used, including, but not limited to, visible light cameras, spectrometers, multispectral cameras, hyperspectral cameras, mid-wavelength infrared (MWIR) cameras, and Raman spectroscopy cameras.

[0100] Hyperspectral imaging of tissue within a paraffin block allows the unique absorption of paraffin to be identified separately from various tissue reflectance peaks in a single image. With a hyperspectral cube based on 3-5 nm steps in frequency, the specific reflectance peaks of paraffin and tissue can be separated and tissue depth can be identified.

[0101] Multispectral imaging, utilizing an array or series of illumination sources ranging from UV to infrared, can enable measurement of tissue and paraffin responses in unique spectral lines with multiple exposures at different color frequencies that elicit the specific absorption or reflection properties of the tissue.

[0102] In some embodiments, a tissue block may be illuminated with structured light, and the returned light can be used to determine various properties of the tissue block, the tissue sample, or both. For example, the contour or cross-sectional area of ​​the tissue sample or the depth profile of the tissue block can be determined using structuring. In some embodiments, the depth profile is the thickness of buried material to be removed. In some embodiments, removing such thickness can expose the tissue sample to a predetermined standard. In some embodiments, structured light refers to the illumination of the tissue block in a specific pattern. In some embodiments, the structured light may be spatially structured, i.e., the tissue is illuminated in a geometrically structured pattern such as a grid, stripes, concentric circles, etc. In some embodiments, the structured light may be spectrally structured, i.e., the tissue is simultaneously illuminated by light having different wavelengths. In some embodiments, the wavelengths may be selected from different intensities, bands, or colors. In some embodiments, the spectrally structured light can be the same or primarily within the same intensity range (e.g., UV), but have different specific wavelengths within that intensity range. In some embodiments, the spectrally structured light may consist primarily of light from one or more frequency bands, such bands tuned to the optical properties of tissue molecules, including, for example, fluorescence absorption and emission spectra. As an example, wavelength ranges primarily involving UV radiation may produce strong autofluorescence from certain tissue compartments, facilitating subsequent processing steps in the present invention.

[0103] Laser dot scattering can also be used. A green laser source at 515 nm and a diffractive optical element (DOE) are used to create an array of laser dots on a paraffin tissue block, thereby sampling the dispersion across the entire block in a single image. Different DOEs can be used to project different sized laser arrays onto the surface of the block. Alternatively, the block can be moved and one or more images taken to increase the laser dot density on the surface of the block. An image of the tissue block is taken while it is illuminated with the laser DOE. One or more channels of this image can be analyzed to determine light scattering. For example, when a green laser source is used to illuminate the block, the green channel will have the highest response. The gray value of the image can also be used for analysis.

[0104] In some embodiments, multiple cameras are provided adjacent to the block face to simultaneously capture images of the block face. The cameras and their software can use the block's inherent geometric features or surrounding features to orient each image to the same reference geometry. Images from multiple cameras can be used to construct a 3D image of the tissue within the block. Such a 3D image can increase the speed at which the block is sectioned, as it can predetermine the amount of sectioning the block by the microtome.

[0105] Images from multiple cameras can also be used to enhance 2D image quality by merging multiple images taken from different angles. Image clarity will increase as more images are processed to create a single image. This can be used for image enhancement of sample block faces, cut tissue sections, and / or slides with cut tissue sections deposited on them.

[0106] Another way to enhance imaging is to mount the imaging device, e.g., a camera, on a computer-controlled motion stage, which can be moved to various positions. In this way, multiple images of the sample block can be taken from different positions along the stage's motion path. Alternatively, the block or tissue on the glass slide can be moved relative to the camera to have a similar effect. Thus, relative motion of the imaging device with respect to the block or sample can be utilized, where relative motion represents motion of the imaging device, motion of the block or glass slide, or motion of both the imaging device and the block or glass slide. The images can be processed to create a single image or to select images to be utilized for comparative analysis.

[0107] In some embodiments, the imaging device, e.g., a digital camera, is housed within a closed chamber. Within the closed chamber, a radiation source with controlled polarity and wavelength can be provided to illuminate the biological tissue sample inside the closed chamber to enhance imaging. The radiation source can have dynamically adjustable polarity and wavelength while the biological sample is being imaged. Such illumination can be provided for tissue on a sample block and / or cut tissue sections on a slide. The system can include various software algorithms for performing different analyses. For example, an algorithm can be utilized to determine the depth of the biological tissue sample beneath the paraffin, an algorithm can determine the overall or partial 3D shape of the biological tissue embedded within the paraffin, and / or an algorithm can determine the largest surface area cross-section of the biological tissue and the depth of the cross-section. Another algorithm that can be provided is one that extracts physical properties of the biological tissue from an image.

[0108] For example, the algorithm may determine physical properties including, but not limited to, the largest tissue contour, the number of tissue fragments within the sample (paraffin) block, and the depth of each fragment within the block. In some applications, a paraffin block may have multiple fragments of tissue within it. These may be the same tissue cut into multiple fragments or multiple tissue samples collected at multiple points from a patient. Placing multiple tissue fragments within the same block helps laboratories reduce tissue staining costs. The feature (algorithm) ensures that all tissue fragments are cut at the same cross section, i.e., they are in the same plane.

[0109] In some embodiments, a projection system projects an orientation pattern onto the block face, and an identical pattern is projected onto the slide for comparative analysis. Software algorithms can be used to determine the relative orientation of the biological tissue sample within the paraffin block and the tissue on the slide.

[0110] The quality control system for identity matches can be used in conjunction with any of the devices / systems and methods described herein.

[0111] Tissue block analysis

[0112] In some embodiments, one or more images can be taken prior to tissue sectioning of the complete tissue block. In some embodiments, cross-sectional images can be taken at known depths into the tissue block to estimate the location, size, and shape of the tissue within the block. One or more of these images can be used to create a depth profile of the tissue embedded within the tissue block. In some embodiments, an estimated image of the composition of the entire tissue block can be created. The tissue block can be illuminated using a visualization system such as described above, such that the illuminating light causes the tissue inside the tissue block to fluoresce. While various illumination types can be used, in some embodiments, the tissue block can be illuminated with UV light, such that the UV penetrates through the embedding material surrounding the tissue and causes the tissue sample embedded within the embedding material to fluoresce. Thus, the tissue embedded within the embedding material can be fully outlined within the block. This can serve as a baseline image that can be used for various comparisons to the exposed tissue on the transport system and on the face of the tissue block on the slide after transport. An exemplary baseline image of an entire tissue block 132 is shown in Figure 3. As shown, the baseline image 130 includes a tissue sample 134 embedded within an embedding material 136 to form the tissue block 132.

[0113] This baseline image of the total composition of the tissue block can be used in various methods disclosed below. For example, when determining whether a tissue block should be sectioned, a captured image of the block face can be compared to the baseline image. Thus, a comparison can be made between the "sectioned" area of ​​tissue and the "filled" area of ​​tissue from the baseline image as this relates to block sectioning.

[0114] The baseline image can also be used for other quality control analyses. For example, an image of a tissue section cut from a tissue block, on tape, or on a slide can be compared to the baseline image. The tissue section can be compared to the "filled" area in the baseline image to determine the integrity of the tissue section, the completeness of the tissue section, and / or the physical properties of the tissue section, or to confirm that the tissue section originated from a particular block.

[0115] For example, as described in more detail below in connection with Figures 4A-4F, an initial section may have only embedded material (Figure 4A), while subsequent sections (Figures 4B-4F) may include tissue samples, the contours of which in the sections may be compared to expected contours from the baseline image for sectioning, tracking, and mechanical integrity determination. In some embodiments, the system may determine the contours of the tissue on the sample block and the contours of the cut tissue sections on the transport medium or slide to determine if a match exists. Cut.

[0116] Block Sectioning Methodology

[0117] In some embodiments, systems and methods for sectioning biological sample tissue are provided, including block sectioning determination to determine when a tissue layer embedded in paraffin or other embedding material has been reached, i.e., facilitating and improving detection of complete sectioning of the tissue block. In some embodiments, this can include a determination system and method for tissue block sectioning assessment and detection in an automated device. The system / method increases the speed of sectioning and the quality of the final section. In some embodiments, sectioning a tissue block is related to the amount of embedded material that needs to be removed. For example, a depth profile of the tissue block can be used, and thus the depth profile is related to the thickness of embedded material that can be removed to expose the tissue sample up to a predetermined criterion related to the distance between the surface of the embedded material and the tissue sample. For example, the predetermined criterion can be the amount or depth of material that, when removed from the face of the block, can reach the surface of the tissue sample, or the predetermined criterion can be the amount of material that, when removed, reveals a sufficient cross-section of the tissue sample on the face of the block. The cross-sectional area of ​​the exposed tissue can vary. In some embodiments, the criterion can be 20% to 60% of the cross-sectional area of ​​the tissue sample. In some embodiments, the reference may be 20% to 80% of the cross-sectional area of ​​the tissue sample. In some embodiments, the reference may be 40% to 60% of the cross-sectional area of ​​the tissue sample. It should be understood that the amount of cross-sectional area of ​​the tissue sample that is exposed may vary and may be any amount.

[0118] In some embodiments, image-based determination systems and methods for tissue block sectioning assessment and detection can be used. Machine vision systems can be used to facilitate and improve block fragmentation determination, i.e., detection of complete sectioning of the tissue block, to determine when a tissue layer embedded in paraffin has been reached. This machine vision system for automating block sectioning determination has application in automating the transfer of cut tissue sections to a support (carrier) medium, such as tape, for subsequent transfer to a microscope slide. In some embodiments, a computational processing system and method are provided after a visualization system utilizing an optical system as disclosed herein is operated. Thus, the visualization system utilizes appropriate optical systems (illumination system / method, imaging system / method, detection system / method), followed by computational processing. This computational processing provides a comparative assessment of images to determine the status of block sectioning.

[0119] In some embodiments, an illumination and imaging system can be used to increase the contrast between tissue sections and paraffin sections of a tissue block, as shown in the image progression in Figures 4A-4F. For example, the illumination system can emit illumination wavelengths to enhance the contrast between the tissue and paraffin. In some embodiments, this allows the system to determine the sectioning status of a block containing a tissue sample embedded within an embedding material. The method includes: a) increasing the contrast between the tissue and the embedded material to enhance the distinction between the tissue and the embedded material, which may include illuminating (e.g., using UV radiation) one or more of: i) the block face of the tissue sample block; ii) the section transport medium; or iii) the slide; b) imaging the tissue and the embedded material; c) processing the images to assess when the block is sectioned; and d) transferring the tissue to a tissue transport medium after the block is sectioned. The progression shows five images as examples to illustrate the process from the initial unprocessed block in Image 1 to the fully sectioned block in Image 5. 4A-4F illustrate a series of six images; however, it should be understood that any number of images can be used to achieve the purpose. Six images are shown for ease of illustration. More specifically, in the images shown in FIGS. 4A and 4B, the target tissue section is completely covered with paraffin; therefore, the first n sections will have no tissue sample, followed by sections with a faint outline of discernible tissue. In the image shown in FIG. 4C, a section of paraffin has been removed, but the tissue is still covered with paraffin, but a larger tissue outline is shown. In the image shown in FIG. 4D, more paraffin has been removed, but a thin layer of paraffin still exists across the tissue. In the image shown in FIG. 4E, the tissue section is shown within a white outline, with paraffin still around the edges (outside the boundary / perimeter defined by the outline), and in the image shown in FIG. 4F, a fully sectioned block is illustrated, with the entire tissue section exposed.It should be noted that the paraffin block is shown schematically as having a planar upper (exposed) surface; however, it should be understood that the block does not necessarily have a flat surface as shown.

[0120] The sectioning determination can be accomplished manually or using an automated system. In some embodiments, an automated system for determining the sectioning status of a block containing a tissue sample embedded in an embedding material is provided in an automated device, including an imaging device for distinguishing the tissue from the embedding material, such as paraffin. In response to distinguishing the tissue and the embedding material, the device determines when the block is fully sectioned. In response to determining when the block is fully sectioned, the device automatically cuts and transfers a section of tissue from the block for subsequent analysis. In some embodiments, after determining that sectioning of the block is complete, the system automatically stops sectioning. In some embodiments, after determining that sectioning of the block is complete and the system automatically stops sectioning, cutting and transferring the tissue section to tape automatically begins, and the tissue section can be mounted on a slide.

[0121] Various parameters / characteristics can be used to assess the sectioning status of the block and make a determination as to whether the block is fully sectioned. In some embodiments, the characteristics of the sample block or tissue section can be determined after it is cut from the block. In some embodiments, an evaluation, e.g., measurement, of the sample block itself or the cut tissue section itself can be performed. In some embodiments, a comparative analysis of the sample block or cut tissue section can be performed against a pre-evaluation, e.g., measurement. In some embodiments, the sample block can be cut to a predetermined depth. It should be understood that any combination of these various parameters / characteristics can be used to make the sectioning determination.

[0122] In some embodiments, as will be discussed in more detail below, an automated system is provided to enhance / facilitate block sectioning determination in an automated tissue transfer device, where the sample block is sectioned and the tissue is transferred to tape or other medium and then to a glass substrate suitable for microscopic analysis after further processing.

[0123] The sample block can be inspected from a variety of angles, such as perpendicular to the front face, at a glancing angle, perpendicular to the side, or at a glancing angle, or a combination thereof.

[0124] Block measurements can be used, or cut sections only can be used, or both can be combined.

[0125] In some embodiments, automated decision-making regarding block sectioning is achieved by enhancing the distinction between paraffin and tissue and determining when block sectioning is complete via an imaging system. In some embodiments, this can be achieved using the illumination and imaging systems described herein. The illumination system can assist in the discrimination of tissue and paraffin, which can then be imaged by the imaging system for evaluation. Thus, the distinction of tissue from paraffin is enhanced, and images are taken on the block, holder, tape, and / or other locations. For example, a machine vision system can enhance assessment when a tissue layer embedded in paraffin is reached, i.e., when a thick section of paraffin wax above the tissue sample on the sample block is removed to expose the tissue sample so that it can be sectioned, transferred to a glass slide, and further processed for evaluation.

[0126] As shown in FIG. 5 , in some embodiments, a baseline image of the tissue sample can be used to assist in sectioning decisions. In particular, in step 140, the cross-sectional area of ​​the filled tissue can be determined using UV fluorescence to create a baseline image. In step 142, as tissue sections are removed from the tissue block, the sectioned area of ​​the tissue can be determined using one of many alternative methods. In step 144, the baseline image and the image of the block face can be compared to make a decision regarding sectioning. For example, as shown in FIGS. 4A-4F , as progressive sections are removed from the tissue block, the contours of the tissue sample within these sections will progressively change. In some embodiments, the system can determine when sectioning is complete based on the expected contour of the tissue sample based on knowledge of the baseline image. For example, sectioning can be completed when only the top portion of the tissue is reached. Alternatively, sectioning may be completed when the middle section of the tissue sample is reached. Such a determination can be made by comparing the contour of the tissue sample in the section to the expected contour of the tissue sample from the baseline image. In step 146, the area of ​​filled tissue is compared to the section area on the tape (eg, using a UV illumination image on the tape) to confirm the sectioning decision made in step 144.

[0127] In some embodiments, a UV method / system can be utilized for the sectioning decision, as shown in the flowchart of FIG. 6 . The steps are as follows: i) illumination with a preselected range of wavelengths (e.g., the UV range) (step 150); ii) using appropriate optics to create an image on a color camera (i.e., a camera that simultaneously captures images in multiple wavelength ranges, such as an RGB camera) in step 152; iii) using color and intensity information from the resulting image to segment and isolate portions of the block where tissue resides in step 154; iv) monitoring the size and edges of the tissue region as the sectioning cut is made in step 156; and v) detecting appropriate changes in the monitored quantities in step (iv), which leads to a “sectioning decision” in step 158. As discussed above, these steps are automated and do not require user input during the process. Note that intensity in grayscale can be used as a substitute for a color image. FIGS. 7 and 8 are example images of a tissue ribbon under UV illumination.

[0128] In some embodiments, as shown in the flowchart of FIG. 9, observations of both the block face and the cut ribbon are made, although UV radiation or other wavelengths can be used to enhance tissue / paraffin contrast. After applying light at the illumination wavelength in step 160, the imaging system creates color images of the block face (step 162) and the cut ribbon (step 164). In this method, the first appearance of tissue fluorescence in the cut section signals that "sectioning" has occurred. This can be done either based on total fluorescence from the ribbon in step 166 (so that there is no need to image the ribbon completely face-up), or alternatively, the ribbon can be imaged face-up in step 168. Such imaging can, in some embodiments, be facilitated by having the ribbon on tape and comparing an image of the ribbon with an image of the block face (each using UV illumination). The images are processed and evaluated for tissue segmentation (or other characteristics / parameters described herein) in step 170 so that the size and edges of the tissue regions can be assessed and quantified (step 172) and changes can be detected to determine the status and completion of sectioning (step 174). In another alternative, imaging is performed only on the cut ribbon, e.g., when on and / or off the tape, e.g., as an alternative to block imaging rather than as a supplement.

[0129] The flowchart of FIG. 10 illustrates various systems that may be utilized as examples for determining block sectioning for unprocessed or partially sectioned blocks (step 180) or fully sectioned blocks (step 182).

[0130] Various methods exist for cutting into tissue blocks to expose tissue embedded within paraffin or other embedding material. Tissue evaluation can be performed on the sample block itself, after sectioning from the block, or both. In some embodiments, a predetermined amount of paraffin can be removed from the tissue block to expose the tissue. For example, in unprocessed or partially sectioned blocks (the latter may result, for example, from a failed sectioning procedure in a previous step), determination of the sectioned block can be made by taking N sections at M μm thickness for fixed / preprogrammed depth paraffin removal (step 184). After such sectioning, block sectioning is considered complete (step 186).

[0131] In some embodiments, an evaluation of the tissue block is performed after a series of, or one or more, cuts are made in the tissue block to determine whether the block has been sectioned after each cut. Sections are cut from the block, and through imaging or other techniques of the block, the cut tissue sections, and / or the cut tissue sections on tape (or other transport medium), the sections are evaluated until a determination is made that the block has been completely sectioned. For example, X sections at Y μm thickness are taken (step 190), then the sections are cut from the block (step 192), and an evaluation of the cut sections is performed (step 194) to confirm that the block has been sectioned (step 196). This check can be by taking images of the cut tissue sections or the cut tissue sections on tape (or other transport medium).

[0132] An evaluation, e.g., measurement (step 202), of the sample block and / or cut tissue (on or off the tape) can be performed with each cut section (step 200), which then leads to a decision to continue sectioning (not yet sectioned) or to stop sectioning (fully sectioned as in step 204). In some embodiments, the decision to continue sectioning can lead to a decision to cut several sections before evaluation, e.g., measurement. In some embodiments, several consecutive sections can be cut before leading to an evaluation or decision.

[0133] In some embodiments, the determination can be made based on an evaluation of the sample block and / or a specific cut section (on or off the tape). In some embodiments, the determination can be made by comparing a second measurement (or other criterion or parameter) to a first measurement (or other criterion or parameter) according to an algorithm. The determination can also be made based on a fixed depth rather than an evaluation of a specific block face or cut section.

[0134] In some embodiments, the depth measurement can be used to (a priori) determine the tissue depth below the embedding material, such as paraffin (step 210). In some embodiments, the tissue depth can be determined from a baseline image, for example, as shown in FIGS. 4A-4F. 3D imaging techniques can be used, for example, to determine the tissue depth without any further measurements. The sample block is cut to the measured depth to expose the entire surface of the tissue in step 212. At this point, the block can be considered fully sectioned (step 214). In some embodiments, after the sample block is cut to the predetermined depth, additional images can be taken in steps 216 and 218, for example, images of the cut tissue section on tape (or other transport medium) to confirm that the entire surface has been reached. In some embodiments, the depth measurement can be used to determine the tissue depth below the embedding material in step 220. After the sample block is cut to a predetermined depth in step 222, a section is cut from the block (step 224) and evaluated to confirm that the block has been sectioned in step 226, for example, by an image of the cut tissue section or the cut tissue section on tape (or other transport medium). If it has not been fully sectioned, another section is cut from the block and checked. This continues until a determination is made in step 228 that the block has been sectioned. It should be understood that other methods can also be used to determine depth, including, but not limited to, ultrasound, x-ray imaging, and other non-light-based detection methods, as well as comparison with a baseline image. One way to accomplish this is with an imaging device that creates multiple images.

[0135] As noted above, in some embodiments, determining when block sectioning has occurred is accomplished by monitoring the paraffin above the tissue section by using a signature of the paraffin that distinguishes it from the tissue. Using this signature, it can be detected when all the paraffin has been removed and sufficient tissue has been exposed, which will then trigger the determination that the "block has been sectioned." Various methods can be utilized for such detection, and two methods for determining the depth of paraffin above the tissue are discussed herein as examples.

[0136] In some embodiments, the block is illuminated with infrared radiation and an image is taken, e.g., at 2,800-3,000 cm^. -1 Infrared illumination in the wavenumber range (3.3-3.6 mu optical wavelength range) can be used because paraffin has strong absorption in this range due to C-H bond stretching modes. If the block is narrowly illuminated in this spectral range (such as by using a quantum cascade-type laser such as a narrowband QC laser at 3.28 mu) and images are taken with an infrared camera, the block will initially appear black (when the entire block face is paraffin), and then brighter areas will appear around the area where the tissue is exposed as the block is cut.

[0137] Based on the fact that paraffin scatters light, in some embodiments, a single sharp spot of light (or an array thereof) is shone on the block face. When looking at the diffusely reflected light, the "spot size" should correlate with the depth of the paraffin, with thicker paraffin meaning the light will be more diffuse. For example, if UV illumination is used (e.g., using a laser with a sharp optical spot), this will generate a point source of fluorescence within the block. Scattering of the UV light on entry and scattering of the fluorescence on exit will also make the spot wider / more diffuse. Thus, the spot size of the fluorescent emission will correspond to the thickness of the paraffin, thus providing a method for monitoring the depth of the paraffin.

[0138] As explained above, hyperspectral imaging can be used with the illumination system. Figures 11A and 11B illustrate an example image of adipose tissue 230 embedded in paraffin 232 and its associated hyperspectral cube. The low count of the adipose tissue layer compared to the paraffin indicates that it is still below the paraffin in the block. The significantly higher tissue reflectance in Figures 12A and 12B indicates that it is at the surface. In this way, the tissue layer depth can be identified.

[0139] As discussed above, laser dot diffusion using diffractive optical elements can be used for imaging, which can determine depth. For example, FIG. 13 shows the green channel of a tissue block image. Using image processing tools, the gray values ​​of the image can be extracted as shown in FIG. 14, which illustrates two dots sampled at one pixel across a block of laser dots on the tissue block. Here, a single pixel column across the dots is sampled. When the gray value falls below a certain count due to tissue absorption, e.g., 20 in this case, that area of ​​tissue can be declared sectioned. The area between peaks 2-4 indicates the sectioned region in FIG. 14. The gray values ​​from each row can be combined to obtain a 3D map of tissue sectioning metrics across the surface of the block. In other words, this method can be used as an absolute measure of sectioning without incremental images. However, using this method with incremental images improves its efficiency.

[0140] The method may include other illumination modalities, such as UV or white light, to determine tissue boundaries within the paraffin block. These boundaries can be used as a mask that can be overlaid onto images acquired using the laser dot array. This refined pixel range helps improve the accuracy of the sectioning decision-making algorithm.

[0141] In some embodiments, the system can be used with a block that has already been sectioned. N sections at mm thickness are created to complete the block sectioning. After the block is sectioned, it can be removed from the microtome and hydrated. After hydration, it is placed back on the microtome. Tissue within the block may absorb more water than the paraffin and may protrude irregularly from the paraffin matrix. It is also highly likely that blades will be changed on the microtome between sectioning and sectioning. The paraffin block will need to be aligned with the blade after polishing when sections are taken that will be stained and analyzed by a pathologist.

[0142] In some embodiments of the automated system, once the block is sectioned, the automated device will automatically stop sectioning and begin taking sections from the tissue block for transfer to tape. Thus, the automated sectioning device is programmed to take tissue sections from the block face once it determines that the block is sectioned, and this transition occurs without any user intervention or input. In some embodiments, once the automated determination that the block is sectioned is made, the automated device will automatically stop sectioning, but user input is required to begin the tissue sectioning / transfer to tape process. The system can include feedback to indicate when the block is fully sectioned.

[0143] In some embodiments, the micro-serrations 240 (referred to herein as "blade ballistics") that the blade leaves on the block face are evaluated to make sectioning decisions, as illustrated in FIG. 15 . On the initial cut section from the sample block, the blade serrations will be present only on a portion of the block. However, when the block is sectioned, the serrations will span the entire block face. This is because the block is cut with a sharp blade, but the block surface is not flat. On the tissue itself, the serrations are interrupted because the tissue's reflection coefficient is different from that of the paraffin block. More specifically, even the best blades have imperfections that leave marks (blade ballistics) on the tissue block during sectioning. These marks will initially be present on a portion of the block because the block face is not flat and cannot be perfectly aligned with the blade. In progressive images, the blade ballistics (serrations) are left on the block face over increasingly larger areas of the block as deeper cuts are made. In other words, when sectioning a block, the entire surface is not polished at once. As it is polished, imperfections in the block appear as thin lines on the block. When the entire surface of the block is reached, micro-serration lines are present over the entire area of ​​the paraffin block. The reflection of the blade trajectory line is different on the paraffin and on the tissue due to different reflection constants. The system compares a normal image of the tissue and an image captured by the blade trajectory method. This comparison provides a quantitative metric of how much the block has sectioned, and thus can identify if / when the block has been completely sectioned. It should be noted that these micro-serrations are not visible under white light, but are visible when illuminated in UV wavelengths; therefore, the illumination system disclosed herein can be utilized with the present imaging system for blade micro-serrations.

[0144] In some embodiments, successive images are taken and compared to prior images by an image processing device. In some embodiments, comparing successive images to one or more previous images assesses color changes over time as the block is cut. In some embodiments, the size and margins of the tissue and / or paraffin are evaluated to assess status. In some embodiments, qualitative changes in image color are evaluated and quantified. In some embodiments, physical properties of the tissue, such as shape, size, margins, and contours, are determined / evaluated to assess status. In some embodiments, physical properties of the tissue are extracted from the images, including the number of tissue fragments in the sample block and the depth of each tissue fragment.

[0145] For fully sectioned blocks, this can be beneficial if the entire rectangular paraffin region of the block profile is captured, not just the tissue. For example, a rhomboid profile can be considered "sectioned" for traditional sectioning if sufficient tissue cross-sections are captured, but only the corners of the paraffin are not. The same is not true for tape transfer, as tape is applied across the entire block and would catch on the blade when sectioning at the corners of the recessed block. Therefore, determining where paraffin is missing would be beneficial. That is, viewing the paraffin material that has been removed can be beneficial. This is because, if a piece is missing mid-cut, the blade will not make contact, and therefore the cut will be deeper. This visualization / evaluation can be achieved by using a video or series of photographs of the block as it is cut to make a sectioning determination, i.e., by viewing the cut material or trimming as it forms away from the blade edge during cutting. The trimming is formed where the blade makes contact. Viewing the blade and where the trimming will occur, i.e., how the blade interacts with the block face at the edge, is similar to performing a line scan of where the blade contacts the block. Images of where the trimming will occur vertically on the block can be useful. For example, if a previously sectioned block has a sunken area in the middle of the tissue from drying, it can be difficult to tell from a photograph. The tissue may be depressed a few microns around the surrounding paraffin, preserving the luster of the sectioned block. It is easier to perform a test cut across the entire block to check whether trimming has occurred.

[0146] There may be instances where tissue is only slightly warped in an otherwise fully sectioned block. Sections are not taken immediately after sectioning; rather, there is a hydration period, usually about 5-15 minutes in ice water, which tends to slightly alter, e.g., warp, the previously sectioned block. Typically, several disposable polished sections are taken to repopulate the sectioned block, but imaging systems may result in fewer wasted sections being taken.

[0147] In some embodiments, an algorithm can process the image collected at each section. It will compare it to one or more historical (prior) images and determine whether the images change in a way that indicates the block has been sectioned. The system can take progressive images of the block as it is sectioned. In parallel, the image processing system will evaluate each image, compare it to historical images from the same tissue block, and decide to continue or stop sectioning the block. For example, a hue value can be detected in the initial unprocessed block, and as sections are cut, the hue value is compared to the initial value. The algorithm can subtract the value of successive images from the initial value, and if it exceeds a predetermined value (error function), the system recognizes the block as having been sectioned. Note that hue is just one example of a detection-based parameter for the algorithm, as other characteristics, as described above, can alternatively or additionally form the initial baseline for the comparative calculation / assessment of successive images to determine the status and completion of block sectioning. Other algorithms can use intensity changes between images at approximately the same location to determine sectioning. On unprocessed blocks (tissue blocks that have not been sectioned), due to the diffuse nature of the paraffin layer on top of the tissue, the image of the tissue will not be clear and the tissue boundary will be fuzzy. In technical terms, the intensity change between the paraffin and tissue boundary will be gradual. As the tissue is sectioned and progressive images are taken, the paraffin layer across the tissue will become thinner and thinner until it is completely removed. When calculating the intensity at the paraffin-tissue boundary in these images, the boundary will become increasingly clearer. With a suitable threshold, it is possible to determine whether the tissue has been sectioned.

[0148] In some embodiments, people may teach the algorithm when the block is being sectioned. Thus, in this alternative embodiment, unlike the previous embodiment, subjective input by people, e.g., users, provides the initial input. In machine learning type algorithms, progressive images taken as more cuts are made must be annotated by a person to indicate whether sectioning is being achieved. This paragraph refers to these annotations.

[0149] In some embodiments, 2D or 3D images may be utilized.

[0150] The block can, in some embodiments, be moved up and down in front of the imaging device. Alternatively, the imaging device can be moved relative to the sample block, or both the sample block and the imaging device can be moved relative to each other.

[0151] As shown in FIG. 2 and described above, the imaging system takes images of the tissue block to assess when sectioning has occurred. In some embodiments, images of the tissue on the blade holder are taken instead or in addition. That is, the imaging system takes images of the cut tissue section positioned on the blade holder. The initial cut section will be tissue-free because unprocessed tissue blocks have a layer of paraffin over the tissue. As explained above, multiple cuts are required to remove this paraffin layer by layer to expose the tissue (see FIGS. 4A-4F). However, as the cut section progresses deeper into the sample block and portions of the tissue begin to be cut, contrast-enhancing illumination utilizing one or more of the illumination systems described herein will enable the capture of tissue images of thin cut sections (ribbons) on the blade holder. That is, under contrast-enhancing illumination, the initial section (which contains all or most of the paraffin) will not fluoresce, but as portions of the tissue are cut, the system will begin to detect these tissue portions. When the tissue on the ribbon resembles the contour of the tissue on the block, the system recognizes that the block has been sectioned. The imaging system in this embodiment will image the tissue block and have an image of the entire surface of the tissue. By comparing this image of the entire surface from the tissue block and images collected from layers removed during the sectioning operation on the blade holder, the system will determine how close tissue sectioning is to being achieved, so that the automated determination of complete sectioning can be influenced. The system / images can also check that the paraffin portion of the section matches the profile of the block to prevent tape snags. In an automated system, once this recognizes that the block has been sectioned, in some embodiments, the device can automatically stop sectioning, i.e., the microtome can stop cutting sections.

[0152] Regarding light-field imaging, in general terms, a light-field camera captures the intensity of light in a scene and also the direction in which light rays are traveling in space. This is in contrast to traditional cameras, which only record light intensity. One type of light-field camera uses an array of microlenses placed in front of an otherwise traditional image sensor to sense intensity, color, and directional information. From this super-resolution variation spatial information, precise identification of the "depth" of tissue located within the paraffin can be obtained. Various illuminations, multispectral, hyperspectral, and UV, can be utilized to bring out the tissue within the paraffin.

[0153] Regarding depth from disparity, depth information can be obtained from 2D images by combining at least two 2D images taken from different positions relative to the object. While keeping the camera in a fixed position, the paraffin block can be moved in a vertical and / or horizontal plane to take multiple images. 3D features of the object can then be calculated based on the 2D images. Image processing tools can be used to determine depth information from multiple images of the same object. Algorithms can detect key points between the stereo images to calculate disparity. This information can then be used to calculate depth information.

[0154] Another method for identifying the depth of a tissue set embedded within a paraffin block, relative to the depth from focus, is to use the optical design of the imaging system to identify the depth of a focused tissue section inside the paraffin block. UV illumination fluorescence imaging allows for the capture of tissue located "inside" an untreated block of paraffin. A series of images of the tissue can be acquired using a stepwise method of moving the block forward toward the imaging system. UV illumination will penetrate the untreated block, causing the tissue to fluoresce. The imaging system is configured with a short depth of focus (DoF). A series of sequential images are then captured as the paraffin block is moved forward in the Z axis toward the camera system in steps equal to the DoF at which fluorescing tissue will be imaged in focus at a given depth. An edge detection algorithm running on the green channel (grayscale) image attempts to identify the image with the greatest number of "edges" or focused details, thus identifying when the majority of the tissue is in focus from the series of displaced images. This is then correlated to the amount the block holder has moved forward, taking into account that depth is modified by the refractive index (RI) of the paraffin wax in its solid form. This a priori calculated depth number can then be used to identify the number of slices cut on the block facing the microtome required to reach the "sectioned" condition. This is a faster method for sectioning a block because it does not require incremental images.

[0155] As discussed herein, the illumination system can include, for example, UV, IR, or visible / broadband. Also, in some embodiments, the imaging system can capture images of one or more of the illuminated tissue block face, a cutting ribbon on a blade holder, or a cut tissue section attached to a support medium such as tape, or a cut tissue section on a slide. In some embodiments, the image can be a video of the block face or ribbon during sectioning. A computational system processes the image, e.g., quantitatively, to determine when the block is sectioned. At that point, the microtome-cut section from the sample block can be automatically transferred to tape by an apparatus component in an automated tape transfer system for subsequent analysis of the tissue.

[0156] The systems herein can also have a linked database for storing data from block sectioning to enable machine learning refinements.

[0157] Comparative and mechanical analysis

[0158] The present disclosure provides systems and methods for quality control in histology systems. In some embodiments, a method is provided that includes receiving a tissue block comprising a tissue sample embedded in an embedding material, imaging the tissue block to create first imaging data of the tissue sample in a tissue section on the tissue block, removing the tissue section from the tissue block, the tissue section comprising a portion of the tissue sample, imaging the tissue section to create second imaging data of the tissue sample in the tissue section, and comparing the first imaging data with the second imaging data to confirm correspondence of the tissue sample in the first imaging data and the second imaging data based on one or more quality control parameters.

[0159] In some embodiments, if there is no correspondence between one or more quality control parameters of the tissue sample in the first imaging data and the second imaging data, the tissue section is unacceptable. In some embodiments, the one or more quality control parameters include one or more of tissue sample shape, tissue sample size, or one or more mechanical damage. In some embodiments, the method can further include transferring the tissue section to a slide using a transfer medium, and the second imaging data comprises imaging data of the tissue section on the transfer medium or imaging data of the tissue section on the slide. In some embodiments, the method can further include comparing at least two of the first imaging data, the imaging data of the tissue section on the transfer medium, or the imaging data of the tissue section on the slide.

[0160] In some embodiments, if there is no correspondence in shape or size between the tissue sample in the first imaging data and the second imaging data, the tissue section is rejected. In some embodiments, the one or more mechanical damages are selected from the group consisting of tears, shreds, blade marks, wrinkles, cracks, bubbles, insufficient tissue sample, and incomplete tissue sample. In some embodiments, the method further includes identifying the tissue section as rejected if one or more mechanical damages are present in the tissue sample in the second imaging data but not in the tissue sample in the first imaging data. In some embodiments, the method further includes adjusting one or more operating parameters associated with removing the tissue section to correct for the one or more mechanical damages. In some embodiments, the method further includes approving the tissue section if no mechanical damage is present in the tissue sample in the first imaging data and the second imaging data. In some embodiments, the method further includes rejecting the tissue block if one or more mechanical damages are present in both the first imaging data and the second imaging data.

[0161] After the block sectioning decision is made, the cut tissue section from the sample block is transferred to tape or other transport medium, and subsequently transferred from the tape or other medium to a glass slide. The system can ensure one or more of the following: i) the section is not mechanically lost and remains properly associated with the sample block (sample tracking); ii) the section is not mechanically damaged, such as wrinkled, torn, cracked, or partially harvested, making it suitable for working with, e.g., suitable for pathology / histology; iii) the section placed on the slide contains a sufficient amount of tissue and not too much paraffin to ensure it is suitable for working with; and / or iv) the multi-fragment tissue within the sample block is fully represented on the slide.

[0162] An exemplary embodiment of a system and method for mechanical quality control of tissue samples is shown in FIG. 16. Such a system can be configured to provide various types / aspects of quality control, including i) comparative analysis 250 of sections on a transfer medium to a slide or sample block or sections immediately after being cut from the sample block to ensure proper correspondence exists (e.g., checking to ensure that the section was not mechanically lost and remains properly associated with the sample block from which it was cut), and / or ii) check 252 to ensure that the cut section on the slide or transfer medium is free of mechanical damage, such as wrinkles, tears, or cracks, that may adversely affect pathology, iii) check 254 to ensure that the cut section on the slide or transfer medium contains sufficient tissue, and / or iv) check 256 to ensure that the multi-fragment tissue of the sample block is fully represented on the slide. These multiple aspects can be used alone, in combination with one of the other aspects, or in combination with two or more of the other aspects.

[0163] Various quality control analyses can be performed on tissue samples during microtomy, including, but not limited to: i) comparative analysis of sections on the slide or transfer medium to the sample block or immediately after cutting from the sample block to ensure that there is an appropriate correspondence (e.g., a check to ensure that the section was not mechanically lost and that it remains properly associated with the sample block from which it was cut); and / or ii) checking to ensure that the cut sections on the slides or transport media are free of mechanical damage such as wrinkles, tears, cracks, etc. that may adversely affect the pathology; iii) checking to ensure that the cut sections on the slides or transport media contain sufficient tissue; and / or iv) Checking to ensure that the multi-fragment tissue of the sample block is fully represented on the slide. These various quality control assays can be used alone or in any combination thereof.

[0164] In some embodiments, a system is provided for checking the condition of the tissue on the microscope slide, which provides another aspect of quality control to ensure that the tissue on the slide is in proper condition for further analysis / evaluation.

[0165] In some embodiments, a system is provided to check whether the section on the slide contains a sufficient amount of tissue to make it suitable for analysis / evaluation. That is, the system ensures that there is not too much embedding material, e.g., paraffin, in the section on the slide. This provides another aspect of quality control to ensure that the tissue on the slide is in proper condition for further analysis / evaluation.

[0166] In some embodiments, a system is provided for checking tissue on tape (or other transport medium) as an intermediate quality control check, for example, for tracking purposes or for tissue integrity purposes (in proper conditions for analysis).

[0167] In some embodiments, a system is provided to check that multi-fragment tissue within a sample block is completely represented on the slide and to ensure that no fragments are missing. Such missing fragments may require the pathologist to request resectioning. This completeness check provides another aspect of quality control.

[0168] In some embodiments, tissue comparison can be facilitated by the illumination subsystem and the imaging subsystem. In some embodiments, this can be provided in an automated transport system, which is described in more detail below. Thus, an image-based automated tissue comparison system is provided within an automated sectioning and cutting tissue transport device, i.e., a machine vision system for automating tracking and quality control of tissue sections. This system can be used to compare the tissue contour on the glass slide with the tissue shape on the block face to ensure proper identification of the slide. In some embodiments, an image of the cut tissue section is captured on a transport medium, which, via a controller, transports the cut tissue section away from the sample block. In some embodiments, the comparing step includes determining the tissue contour on the sample block and the contour of the first cut tissue section. In these systems, an image of the block face can be captured immediately before the tissue section is harvested (or alternatively, or in addition, an image of the slice is captured after it has been cut from the sample block), and the image is used as a comparison image for subsequent images of the same section on the slide. The calculating step compares the two images to ensure there are no significant changes in one or more parameters or characteristics. If a significant change is detected, for example, if the change exceeds a predetermined parameter in some embodiments, this can be provided as a feedback signal for corrective action. The illumination system assists in the discrimination / differentiation of tissue and paraffin, which can be imaged by the imaging system for evaluation. Thus, in the present systems and methods, differentiation of tissue from paraffin is enhanced and images are taken on blocks, transport media, slides, and / or other locations. For example, comparing the images includes assessing and quantifying changes in image color. In some embodiments, comparing the images includes determining whether there are changes in one or more of location, spatial shape, and integrity. In some embodiments, qualitative changes in image color, granularity, etc. are assessed and quantified.In some embodiments, grayscale imaging can be used, so that if the change exceeds predetermined parameters, a feedback signal is provided for corrective action. Various illumination and imaging systems are discussed above.

[0169] Systems and methods for computational processing after a visualization system utilizing an optical system as disclosed herein has been operated can also be provided. Thus, the visualization system utilizes appropriate optical systems (illumination system / method, imaging system / method, detection system / method), followed by computational processing. This computational processing provides comparative assessment of images to determine tracking or other aspects of quality control.

[0170] The illumination system enhances visual / imaging differentiation of tissue and paraffin, and the imaging system captures images of the illuminated tissue / paraffin for subsequent comparison. The illumination system enhances visualization / imaging of tissue on the block face, and the imaging system captures images of the illuminated tissue for subsequent comparison for quality control. Such imaging of individual tissue sections occurs prior to separation of the cut tissue from the block or otherwise prior to transfer to a slide, providing a basis for comparison. Subsequently, such assessment of individual tissue sections occurs after the cut tissue sections have been transferred to a slide. Various methods for differentiation are described below. Various imaging systems and various locations for imaging are also discussed below. Also discussed in detail below are various embodiments of illumination systems that create and / or enhance contrast between tissue and paraffin, depending on the properties of the paraffin and tissue. In some embodiments, the tissue of the sample block is embedded in an embedding material, and the method further includes one or both of the steps of: i) illuminating the sample block with a wavelength of light to increase the contrast between the tissue of the sample block and the embedding medium of the sample block in which the tissue is embedded; and ii) illuminating a first slide and / or transport medium containing the first tissue section with a wavelength of light to increase the contrast between the tissue and the embedding medium in which the tissue is embedded.

[0171] Comparative analysis (block vs. intercept)

[0172] There are various methods for achieving a comparison to determine whether a tissue section on a slide or in transit between a tissue block and a slide is within preset criteria to correspond to the same piece of tissue on the sample block. The system can additionally or alternatively compare a tissue section on a microscope slide to a tissue section just cut from a sample block to determine whether they correspond to the same tissue sample comparison within preset criteria. The tissue section on the transport medium can additionally or alternatively be compared to the tissue on the sample block or microscope slide. The decision system can examine one or more parameters (characteristics / features) to make the comparison. The decision system's decision-making algorithm then provides a cue or potential optional action to take. These quality control systems speed up the process, improve the process through fewer errors, and result in fewer wasted sections. In some embodiments, the comparison determines whether a matching identification exists between the tissue block and the tissue section, and can include matching tissue contours and edges and barcodes on the sample block 260 and slide 262, for example, as shown in Figures 17A and 17B. In some embodiments, the comparison determines a match between the tissue block and the in-transit tissue section, as shown in Figures 18 and 19, which illustrate exemplary images taken from the in-transit tissue section. The following are some examples, and it should be understood that other criteria may also be utilized, for example, utilizing light, composition, mechanical properties, etc.

[0173] It should be understood that instead of comparing the tissue on a slide to the block face, a comparison can be made between the tissue section on the slide and the cut tissue section (slice) after it has been cut from the sample block. Thus, the discussion of systems for assessing the block face, including illumination and imaging systems, discussed herein is fully applicable to assessing the cut slice for comparison to the tissue section on a slide.

[0174] Block sectioning determination, in some embodiments, can be determined in accordance with the inventive concepts in the commonly assigned provisional application entitled "Systems and Methods for Assessment of Tissue Block Facing in Automated Tissue Transfer Systems," filed on the same day as the present application, the entire contents of which are incorporated herein by reference. Other methods can also be utilized. Once the block is sectioned, the block is ready for cutting thin tissue sections for transfer to a transport medium (e.g., tape) and then to slide analysis. Accordingly, the quality control systems / methods disclosed herein can be utilized in conjunction with such block sectioning determination. In some embodiments, automated methods (processes) and systems can be used to automatically section tissue within a paraffin block via a fully automated sectioning device; once sectioned, the tissue is automatically cut from the block face and automatically transferred to the tape, which is automatically moved via rollers to advance the cut tissue and position subsequent portions of the tape across the block face for subsequent transfer of the cut tissue sections to the tape. In some embodiments, the automated tissue sectioning device also includes a slide station, where the tissue sections held on the tape are automatically transported and transferred within the automated device to glass slides for analysis.

[0175] After it is cut from the block and attached to tape, an image of the cut tissue section on the tape (or other transfer medium) can be taken. Additionally, or alternatively, an image of the cut tissue section can be taken after it is transferred from the tape to a slide. An algorithm will process the images collected at each section using a computational step, comparing the image on the tape and / or slide with one or more historical (prior) images to determine whether there are significant changes in properties such as location, spatial shape, and integrity. The location of the tissue section is on a (glass microscope) slide. The tissue section has a rectangular shape, with larger sections measuring approximately 28 mm x 22 mm. The usable area of ​​a glass slide is approximately 50 mm x 25 mm, and the tissue section can be transferred anywhere on the slide, including rotational variations. However, such accidental transfer is undesirable. A mechatronic system can ensure that tissue sections of similar size are deposited in similar locations on the glass slide. In addition, a QC system will check whether the transferred tissue is in the expected location and orientation. Spatial shape can be considered part of the preceding discussion. Tissue integrity refers to the absence of defects such as bubbles, tears, blade marks, shreds, cracks, and missing pieces beneath the tissue. Note that the historical (reference) images can include images of the sample block before it is cut and / or images of the slice after it is cut and before it is placed on the tape or slide. Thus, the system will take progressive images of the block as it is sectioned. The system will also take images of the cut tissue slice on the tape and / or slide. In parallel, the image processing system will evaluate each image and compare it to historical images from the same tissue block to ensure it has not changed. For example, hue values ​​can be detected in the same block, and as the slice is cut, the hue value is compared to an initial value. The algorithm can subtract the value of successive images from the initial value and assess whether this matches.It should be noted that color is merely one example of a detection-based parameter of the algorithm, as other characteristics as described herein may alternatively or additionally form an initial baseline for the comparative calculation / assessment of successive images to determine a match. The intensity change between images at approximately the same location can be used to determine sectioning. On unprocessed blocks (tissue blocks that have not been sectioned), the tissue image will not be clear and the tissue boundary will be fuzzy due to the diffuse nature of the paraffin layer on top of the tissue. In technical terms, the intensity change between the paraffin and tissue boundary will be gradual. As the tissue is sectioned and progressive images are taken, the paraffin layer across the tissue will become thinner and thinner until it is completely removed. When calculating the intensity at the paraffin-tissue boundary in these images, the boundary will become increasingly sharp. With a suitable threshold, it can be determined whether the tissue has been sectioned.

[0176] In some embodiments, the quality control is not a machine learning algorithm trained by people. Thus, in some embodiments, the methodology will not rely on expert humans teaching the machine learning algorithm how to assess quality or match. Note, however, that in some implementations, the results of classical image processing methods may be fed into the machine learning algorithm to train it in the hope that it can handle more general cases. This method would cost-effectively increase the number of annotated images used for the AI ​​algorithm training phase. In machine learning type algorithms, progressive images taken as more cutting is performed would need to be annotated by a person to indicate whether sectioning is being achieved. However, alternatively, classical image processing techniques could be used to annotate images that are easier for such algorithms (which are more structured) to train the AI ​​algorithm and extend the applicability of the overall algorithm to more general (unstructured) data.

[0177] In some embodiments, the illumination system enhances tissue detection. In some cases, processed and embedded tissue has a very faint color compared to the surrounding paraffin matrix, making it difficult to reliably capture the tissue contours using conventional imaging. Therefore, application of a range of wavelengths can increase the contrast of the tissue relative to the paraffin. For example, UV light is used to increase the contrast from 320 nm to 400 nm. Such detection enhancement facilitates comparison of the tissue on the slide (or tape) with the block. This also facilitates checking the suitability of the tissue section on the slide (or tape) according to other quality control aspects.

[0178] In some embodiments, increasing the contrast of tissue from paraffin is achieved by using multispectral images, i.e., various wavelengths of radiation, to illuminate the tissue block in the same instance of block sectioning. These images are combined to increase the contrast of tissue sections within the tissue block. These higher contrast images are easier to compare.

[0179] In some embodiments, UV radiation can be used to illuminate tissue because tissue samples fluoresce when illuminated by UV radiation. As used herein, UV radiation can be broadly interpreted as wavelengths shorter than optically visible blue light. However, it should be noted that in some embodiments, the actual wavelength range available may include portions of the blue end of the light spectrum. Because biological tissues contain numerous fluorescent molecules relevant to this context, including NADH and FADH, tissue samples may glow (e.g., glow green) under diode-based UV illumination. However, paraffin does not fluoresce under the same conditions; the paraffin block may scatter the visible portion of the UV light source and appear a different hue or color, e.g., bluish. Three advantages of UV light can be realized. First, UV light penetrates into the paraffin block, and fluorescent radiation escapes from the paraffin block; therefore, the present method / process allows for clear visualization of tissue samples embedded within the block. This contrasts with viewing the block under visible light, which is strongly scattered by the paraffin wax, making the embedded tissue sample not clearly visible or even invisible. Second, the color (hue) of the emitted light (or, more precisely, the wavelength range of the fluorescent and passively scattered radiation) provides a sharp contrast between the tissue and the paraffin wax, thus allowing for easy detection and segmentation of the tissue sample. Third, by imaging the cut sections on tape (or other transport medium) and / or slides and observing the distinct fluorescent radiation emitted by the tissue, it is possible to precisely detect the tissue placement to check its integrity and ensure that it matches the pre-cut tissue section.

[0180] In some embodiments, another range of illumination wavelengths utilized to illuminate the block face and tape and / or cut tissue sections on slides is located in the infrared range. Paraffin wax has a characteristic infrared absorption spectrum. By selecting tissue portions from processing UV images, when a reflectance spectrum is obtained from the face of the paraffin block in imaging mode (or when reflectance IR spectroscopy is performed in imaging mode), tissue can be detected as the IR spectral signature of paraffin is reduced in a localized manner across the tissue sample.

[0181] Infrared spectroscopy can, in some embodiments, be used to detect the hydration state of tissue within the block, utilizing the characteristic IR absorption spectrum of liquid water.

[0182] One method, utilizing UV or infrared tissue illumination, is shown in the flowchart of FIG. 20 . The steps can include: i) illumination with a preselected range of wavelengths (e.g., the UV range) in step 270; ii) using appropriate optics to create images of the block face (step 272) and the tape and slide (step 274) on a color camera, i.e., a camera that simultaneously captures images in multiple wavelength ranges, such as an RGB camera; iii) using color and intensity information from the resulting images to segment and extract tissue-present areas (step 276); iv) monitoring the size and edges of the tissue regions (step 278); and v) comparing the images to detect conformance / changes (step 280). Optionally, a comparison can also be made between the image and a baseline image (step 282). In particular, as discussed above, the contour of the tissue sample can be compared to the expected contour of the tissue sample from the baseline image, and a comparison of the actual contour and the expected contour can confirm the source of the tissue sample, i.e., that the tissue sample originates from the tissue block having the barcode associated with the slide.

[0183] This information is used to compare the tissue on the tape with the image of the block and the image of the tissue on the tape with the image of the block. These first comparisons (between the tape and the block) allow for the identification of tissue picked up from the block face with the transport medium (tape). The tissue may be partially picked up, or parts of the tissue may be torn and rotated. If the tissue on the tape is not of high enough quality, it is not worthy of being transferred to a glass slide. This saves time and resources. The second comparison (between the slide and the block) involves tissue transferred to a glass slide that may have bubbles, tears, missing fragments, etc. These glass slides should not be given to the end user as a final product because they would be substandard or worthless. The algorithm may result in re-cutting of sections or alert the user to bad blocks. Bad blocks may have tissue that was not properly embedded in the laboratory before being introduced into the system.

[0184] As discussed above, in an automated device, these steps are automated and do not require user input during the process. Note that grayscale intensity can be used as a substitute for color images. Thus, in this method, UV radiation or other wavelengths enhance tissue / paraffin contrast as discussed herein, and observations of both the block face and the cut tissue section are performed. In this method, the appearance of tissue fluorescence in the cut tissue section is detected. This can be done either based on total fluorescence from the ribbon (so that there is no need to completely image the ribbon face-up), or alternatively, the ribbon can be imaged face-up. Such imaging is performed on the cut tissue section (on tape or slide) by comparing an image of the tissue section on the tape or slide with an image of the block face (each with UV illumination). Images are processed and evaluated for tissue segmentation (or other characteristics / parameters described herein) so that the size and edges of the tissue regions can be assessed and quantified until a match is reached.

[0185] In some embodiments, multispectral illumination can be used, involving spectroscopy, i.e., obtaining information from multiple wavelengths or colors; for example, a Fourier transform infrared spectrometer can be employed. This can be done in imaging mode or by simple spectroscopy from a spot selected by some other method (preliminary UV imaging) to focus on top of the tissue. In either case, the goal is to employ the distinctive infrared spectral signatures of paraffin and tissue to (i) determine whether paraffin is present on top of the tissue or whether the paraffin has been removed and the tissue exposed, or (ii) image the ribbon on the tape and detect the presence of tissue and the reduced amount of paraffin, or (iii) image the ribbon on the slide, detached from the tape, and detect the presence of tissue and the reduced amount of paraffin.

[0186] In some embodiments, visible / broadband illumination is used to image the block face and / or tissue sections on tape and / or slides for comparison and (i) detect qualitative changes in the image such as tissue areas becoming more visible / darker brown / with more clearly defined edges on the block, or ii) detect tissue by looking at cut tissue sections and using color / intensity information.

[0187] It should be understood that the above methods may be combined such that more than one lighting system may be utilized.

[0188] In the methods herein, used individually or in combination, there is a calculation step as discussed herein in which the multicolor image or spectrum is analyzed and appropriate changes are detected to ensure that the cut tissue section remains properly associated with the sample block. This calculation step can include image comparison with an original or baseline image or with a prior image, and comparisons of hue, intensity, boundary, etc. can be quantified to calculate the degree of difference between the images for assessment.

[0189] In the case of tissue imaging on tape or on slides, the reference image may be an image of the tissue in the block.

[0190] The automated system in some embodiments can capture various resulting variables such as speed, temperature, humidity, timeout, etc. for input into machine learning to refine the process. If the QC system deems a section to be of good quality and this trend correlates with a range of operating temperatures, this can become the basis for a machine learning algorithm to ensure that all future blocks with similar tissue are cut under conditions that result in good quality cuts.

[0191] The decision-making process can determine that there is no proper correspondence (comment criteria) between the tissue on the slide and the tissue on the sample block. The decision-making process can also include finding a proper correspondence between the tissue on the slide and the sample block, but finding that the tissue is distorted or damaged and therefore unusable.

[0192] Note that the decision-making algorithm may provide cues for recommended actions and following the recommendations may be optional, however, in some embodiments, whether or not the cues are taken, the information is recorded in a database, which can potentially use machine learning to improve the decision-making algorithm.

[0193] In some embodiments, the system can provide a cue for when to select another section to transfer to a slide, for example, selection can be every nth section, or when the images of successive sections change by some fractional amount.

[0194] An example of an inaccurate match will now be described. As discussed herein, biological tissue is embedded in a paraffin matrix (or other embedding material) that forms a sample block. However, tissue embedded in a paraffin block may not necessarily have high contrast compared to the paraffin matrix. This can adversely affect image analysis because it may be more difficult to distinguish between tissue and paraffin, and therefore more difficult to assess the shape, e.g., contour, of the tissue on the sample block. Accordingly, the illumination and imaging systems disclosed herein provide systems and methods for improving the differentiation of tissue and paraffin, such that tissue images, and thus tissue shape, e.g., contour, can be more accurately determined (analyzed). This ensures a more accurate comparison of tissues by, for example, reducing potential distortions of the image due to inaccurately including paraffin as part of the tissue image. In other words, if a "base" or "input" image, defined as an initial image intended to define the tissue contours on the sample block for later comparison with the tissue contours on the slide, contains paraffin, and a "second" or "output" image, defined as a subsequent image of the tissue on the slide, is processed without paraffin, a false determination of a non-match may occur. Similarly, if the base image does not contain paraffin, but a second image of the tissue on the slide is defined with paraffin, a false determination of a non-match may occur. Conversely, if not accurately distinguished and processed, a false match may also occur.

[0195] Section thickness ranges from about 1 to about 15 μm, but is most commonly about 4 μm thick. At this thickness, the contrast ratio between the paraffin matrix and the tissue section is very low. In some embodiments, the contrast ratio between the tissue and the paraffin is enhanced by the systems and methods disclosed herein to ensure that quality control systems accurately compare the tissues themselves or accurately identify the tissue and paraffin on the image. Image post-processing efficiency increases when images have a high contrast ratio, as explained above. When tissue is illuminated with light in a certain wavelength range, it begins to fluoresce, while paraffin does not fluoresce in the same wavelength range. This creates a high-contrast image. Therefore, the sample block is illuminated with light of a range of wavelengths to increase the contrast ratio between the biological tissue and the paraffin matrix. Similarly, the glass slide containing the tissue section deposited thereon is illuminated with light of a range of wavelengths to increase the contrast between the biological tissue and the paraffin matrix. The slide with the tissue can be illuminated from the back, or alternatively, from the front, and the back and front of the slide can be defined based on where the camera is placed relative to the glass slide. Thus, in these embodiments, the system can better distinguish tissue from paraffin for comparative analysis of the sample block and slide.

[0196] In some embodiments, the wavelength of the light can be controlled using filters or LEDs with a given range of wavelength emission. In some embodiments, on the image capture side, filters can be provided to enhance image capture. The set of light source, filter, and camera can be referred to as imaging hardware.

[0197] Mechanical property analysis

[0198] In the illumination and imaging systems disclosed herein, the systems can be utilized to ensure that cut tissue sections do not suffer mechanical damage, such as wrinkles, tears, or cracks, when transferred to a slide. Such systems can also be utilized to ensure that a sufficient amount of tissue is on the slide. When comparing the tissue on the tape or tissue to the block face, if there is a significant difference in surface area, the algorithm can indicate that there is not enough tissue on the slide.

[0199] The composition can be measured by sampling the vapor of the sample or by extracting substances from the sample by bombardment and detected by mass spectrometry, vapor phase chromatography, or other methods. This is in the context of mass spectrometry, in the sense of detecting substances in vapors across substances.

[0200] Mechanical properties can be measured by vibration, atomic force microscopy, or other methods. Vibration can be used to determine material properties, but in this case, it is included here for completeness, even though it is a stretch. In the case of atomic force microscopy, the attractive force on the probe and the material being probed can be used as an indication of material properties. The reason this is included separately is because of the integrity of the cross-sectioning determination sensor; it is not an imaging modality.

[0201] In some embodiments, the quality control system can check sample orientation and / or inversion. In some embodiments, the quality control system determines tissue orientation variations on one or both of the transport medium and the slide and alerts the user if components of the automated device require adjustment.

[0202] Sample sufficiency analysis

[0203] In some embodiments, the system can perform checks to ensure that the cut section on the slide or transport medium contains sufficient tissue. For example, the system will compare the surface area of ​​the tissue in the block face and the section on the glass slide. If the two areas are similar within a predetermined range, tissue integrity is maintained. Another example is the presence of air bubbles under the section. Comparing the intensities of the two images will reveal whether air bubbles are present. This can also provide the location of the air bubbles. If air bubbles are present only within the paraffin matrix, this is not a fatal failure. On the other hand, if air bubbles are present on the tissue, this indicates low-quality tissue on the slide.

[0204] Tissue Sample Integrity

[0205] In some embodiments, the system can perform checks to ensure that multi-fragment tissue in a sample block is fully represented on the slide. In some tissue blocks, there may be multiple fragments of tissue. The histotechnician places the tissue fragments in a plastic cassette and pours warm paraffin wax over them while attempting to push them to the bottom of the cassette. In some cases, some of these tissues shift and are not flush with the rest. During sectioning, one way to verify is to compare the block face image with the tissue on tape or a glass slide. If they have the same number of tissues, overall tissue integrity is maintained.

[0206] Tracking and Printing

[0207] In some embodiments, a just-in-time glass slide label printing protocol can be implemented in which labels for slides are printed after tissue samples are cut from tissue blocks. In this manner, glass slides are barcoded or labeled by a just-in-time printer with barcodes derived from blocks that have just been sectioned in a microtome, and the immediately cut tissue section is then placed on the newly printed barcoded slide. In some embodiments, the next tissue section is cut and a label printed only after the previous tissue section has been placed on the slide, labeled, and optionally confirmed to be associated with the tissue block. In some embodiments, real-time updates are communicated to the device software via a laboratory information management system, also enabling real-time tape marking of barcode data.

[0208] In some embodiments, the present disclosure closes the loop on tracking the cut tissue sample as it passes between the block face and the destination of the glass microscope slide, thereby providing real-time, updatable tracking and identification of the tissue section location in the tissue processing device relative to LIMS data. In some embodiments, the transport system is labeled to associate the tissue section placed on the transport system with the tissue block from which the tissue sample was cut. In some embodiments, the scanned barcode data is tracked from the time the section is placed on the tape, which includes replicating the information with a tape marking / printing mechanism, replicating the barcode data with just-in-time digital printing of indicia on the glass slide, transferring the tissue to the glass slide, scanning the printed barcode on the glass slide, then verifying exact correspondence between the barcode data on the block, the printed tape, and the printed slide, and optionally communicating a summary report to the LIMS.

[0209] The present disclosure is directed to tracking tissue sections cut from a sample block and just-in-time printing of glass slide identification labels for the cut tissue sections in an automated tissue transfer device. Information from the tissue block is transferred to the slide in real time, ensuring accurate one-to-one tracking and labeling of the tissue sections. The present disclosure overcomes the problems and deficiencies of the prior art by implementing a just-in-time glass slide label printing protocol. In particular, one or more tissue sections from the same tissue block are cut before the glass slide is actually printed. The glass slide can then be barcoded or labeled by a just-in-time digital printer using a barcode derived from the tissue block just sectioned in a microtome. The immediately cut tissue section is then placed on the newly printed barcoded slide.

[0210] Tracking and identification of tissue sections can be achieved by several integrated subassemblies and mechanisms, including, by way of non-limiting example, a tape-marking or tape-printing device integrated into the automated tissue sectioning machine that replicates barcode data associated with the incoming tissue block, captured by a barcode reader. Barcode data generated by laboratory information management system (LIMS) software is embodied by printed adhesive labels attached to plastic cassettes holding the tissue blocks. In some embodiments, the tissue transport medium may have location markings or barcodes printed thereon before it is used for tissue transfer. When the tissue transport medium is adhesive tape, location markings can be placed on the tape during a tape transfer operation.

[0211] Typically, a tissue sample (also called a tissue block or sample block) is provided in a plastic cassette and embedded in paraffin wax or a similar material. The plastic cassette provides a feature for the sample block to be held in the microtome clamp. Once the sample block is secured in the microtome clamp for cutting (sectioning), the new block is first sectioned with relatively thick sections, by removing a 0.1 mm to 1 mm layer of paraffin wax from above the tissue sample to expose the tissue sample. After removal of this superficial paraffin layer, the complete contours of the tissue sample are exposed and the block is ready to be sectioned. This process of removing this paraffin layer and exposing a large cross-section of the tissue is referred to as block sectioning. Once the paraffin layer is removed, the tissue is typically sectioned to a thickness of 3 μm to 5 μm in clinical and research settings. That is, once sufficient paraffin has been removed (the block is said to be "sectioned"), subsequent block sectioning provides tissue sections for placement on glass slides for analysis (which are further processed for evaluation). Tissue sections cut from the sample block can be transferred to slides, such as, for example, using a tape transport mechanism. In some embodiments, the process can be automated, as disclosed, for example, in commonly assigned U.S. Publication No. 2017 / 0205317. Other examples of automated devices and variations thereof are disclosed in U.S. Publication Nos. 2017 / 0003309 and 2017 / 0328818, the entire contents of which are incorporated herein by reference. It should be understood that the automated histology device provides an example of an automated device, as the illumination / imaging system and quality control system can be used in conjunction with other automated devices. Also, as discussed herein, the section tracking system can be used in conjunction with manual systems and methods.

[0212] Referring to Figures 17A and 17B, the incoming tissue block includes a label, i.e., a barcode number, attached to the plastic cassette. Barcode data generated by laboratory information management system (LIMS) software provides information about the source of the tissue sample; for example, the barcode information includes an accession number and block ID. In some embodiments, this information can also include the patient name and the date the sample was obtained. Depending on the laboratory, additional information may be included. In addition to the barcode, labels or etchings on the block may include a human-readable alphanumeric version of the data. In some embodiments, the microtomy device communicates with the LIMS, allowing real-time LIMS updates to be made to correctly match the appropriate tissue block from the initial pickup by the robotic arm to the actual tissue sectioning and delivery of the tissue section to the slide. The barcode information on the tissue block, which is optionally updated, is also printed on the slide so that there is a one-to-one correspondence between the tissue section from the tissue block and the slide. As described in more detail below, labels for slides can be printed after the tissue section is cut from the tissue block.

[0213] Referring to FIG. 21A, a barcode reader is provided to scan barcodes associated with incoming tissue blocks. Scanning can occur at the time of tissue sectioning. The barcode information is used to query data from the LIMS and determine the number of sections that need to be cut, the section thickness, and other processing parameters. One or more tissue samples can then be cut by a microtome and transferred to slides, which are also labeled with the barcode data associated with the tissue block to create a one-to-one association between the tissue block metadata and the tissue sections on the slides. In some embodiments, slides are labeled based on tissue block barcodes with iterative variations. For example, if the block barcode is 12345, the barcode for the first slide can be 12345-a, the second can be 12345-b, and so on. Slide labels are printed just in time prior to tissue transfer to slides.

[0214] In some embodiments, the tissue section is transferred to the slide using tape. It should be noted that transfer media (also referred to as transport media) other than tape may also be utilized. Thus, references to tape herein are used for convenience, as the systems and methods disclosed herein are fully applicable to other transport media than just tape.

[0215] In some embodiments, the tape transport system is configured to enable a tracking and identification system. The tape transport system can be marked with information that can be associated with the tissue block. Such marking can be done after the tissue block is received in the device or can be pre-printed on the tape. In some embodiments, the transport medium (tape) can include location markings. A laboratory-assigned block ID can then be associated with this location marking when the tissue section is picked up by the transport medium, and the two IDs can be associated using a software tool. It is also possible that no physical markings are present on the tape, but virtual markings can be inferred based on position encoders in the device, which can track absolute positions on the tape and associate these positions, explicitly or implicitly, with the sections via a suitable control algorithm.

[0216] FIG. 21A is a schematic diagram of some embodiments of a device with an automated tape transport system 300. In some embodiments, the tape transport system is configured to enable a tracking and identification system. FIG. 21A illustrates the path of a tape 302 for transporting cut tissue sections after the block has been fully sectioned. FIG. 21A shows a microtome 304 used to hold a sample block and cut sections. The microtome 304 holds a sample block with tissue samples encapsulated within a support block of embedding material, such as paraffin wax. The microtome 304 includes a blade (not shown) that is aligned to cut slices (or sections) from the face of the tissue block. Once the tissue samples are cut from the tissue block, they are mounted on a tape to be transported to slides.

[0217] The automated microtome device can also include a tape marking system 306, which communicates with a barcode scanning reading system 308. The tape marking system 306 can be used to mark the adhesive tape with barcode information captured from labels attached to the plastic cassette holding the tissue block. Various printing methods, including thermal or continuous inkjet printing techniques, may be used within the automated tissue sectioning device for this purpose. In addition, a thermal transfer printing unit may also be used to generate in situ identification information on the tape that tracks the incoming tissue block to the cut section on the tape; this information then allows for correspondence between the sections on the tape and the sections on the slide, ensuring that the integrity of the sample is maintained.

[0218] The tape transports the tissue sections from the sectioning microtome 304 to the slide station 310. In some embodiments, the device can also include a glass slide printing system 312 and a barcode reading system 314. The printing system 312 prints indicia for the slide that associate the tissue section to be placed on the slide with the tissue block from which the tissue is cut. In some embodiments, the automated system can associate a barcode identifier on the tissue block with a marking on the tape transport medium, and then associate the marking on the transport medium with a barcode that is printed on demand onto the glass slide. This is in the context of a fully automated tissue sectioning device, providing just-in-time printing of real-time LIMS data onto the glass slide. Note that other transport devices / systems can also be used. Tissue in / on these other transport systems can be tracked according to the tape printing system described herein. Thus, the systems described herein, e.g., tape printing system, slide printing system, etc., are fully applicable to sectioning (slicing) on ​​a variety of transport systems. Multiple levels of tracking are provided due to the tracking of tissue at different stages in the device, e.g., from block to new slice, slice during transport, slice on slide. In some embodiments, the label may link the slide to associated LIMS-based information, such as the originating sample tissue block and sectioning date. Tissue blocks may be similarly labeled. To accommodate pre-labeled blocks, an optical reader, such as a barcode reader, may be used to read the block label and generate an associated slide label.

[0219] In some embodiments, the print head of the tape marking device may be installed in the tape path at some arbitrary point before tissue transfer from the tissue block to the tissue transport medium. A barcode reader adjacent to the block plastic cassette reads the barcode data on the plastic cassette so that the barcode data or other alphanumeric data is replicated on the tape transport medium at the time of sectioning. In some embodiments, the marking on the transport medium may not be a duplicate of the barcode on the block cassette, but the two markings may be related through software structures. In some embodiments, information printed / etched on the tape can enable tissue tracking inside the microtome device. The alignment between the block barcode and the tape mark (inside the device) can be ensured by the mechanical operation of the device or by scanning the section with the tape mark, for example, using a camera. The glass slide is printed with a barcode that relates to the barcode on the tissue cassette barcode and then finally scanned, thereby ensuring a one-to-one mapping or correspondence between the barcode data associated with the incoming block and the barcode data printed on the glass slide label, and therefore ensuring tissue sample tracking, an important aspect of regulatory quality assurance.

[0220] In some embodiments, the match between the tissue in the block and the tissue section on the slide can be confirmed based on camera images and image processing. In some embodiments, an imaging or manipulation device can be employed to check that indicia on the slide were printed correctly so that the tissue section on the slide is associated with the correct tissue block. At each point, a physical copy or print of the markings on the tissue-carrying container (block cassette, transport medium, or glass slide) is recorded and cross-checked for correct tracking of the tissue. This provides situational awareness of how the tissue and cut tissue sections traverse through the tissue processing device. In some embodiments, the disclosed methods and systems can utilize a quality control imaging system, such as that disclosed in co-pending U.S. Application No. 62 / 980,203, filed February 22, 2020, which is incorporated herein by reference in its entirety.

[0221] The scanned barcode data is tracked from the time the section is placed on the tape, which includes the steps of replicating the information by a tape marking / printing mechanism, replicating the barcode data by just-in-time printing of indicia on the glass slide, transferring the tissue to the glass slide, scanning the printed barcode on the glass slide, then verifying exact correspondence between the block face, tape, and slide barcode data, and optionally communicating a summary report to a LIMS.

[0222] In some embodiments, the present disclosure also provides a system for checking tissue on tape (or other transport medium) as an intermediate quality control check, for example, for tracking purposes or for tissue integrity purposes (in appropriate conditions for analysis).

[0223] 21B, in some embodiments, the tape can be pre-printed. The transport medium (tape) may be pre-printed with location markings thereon by a conversion process outside of the device. A laboratory-assigned block ID can then be associated with this location marking at the time the tissue section is picked up by the transport medium, and the two IDs can be associated using a software tool, such as by creating a corresponding entry in a database table.

[0224] Referring to the tracking flowchart of FIG. 22 , a barcode associated with an incoming tissue block is scanned at the time of tissue sectioning using an integrated barcode reader (step 320). In some embodiments, to replicate the LIMS-based barcode data associated with the incoming tissue block, the section transport system (e.g., tape) is marked with identifying information (322), which may be identical to the barcode or may include some arbitrary representation of the LIMS data. Additionally or alternatively, the physical location of the tissue section on the tape is tracked by tracking the length of the tape from a reference mark, such as the beginning of the tape. The tissue section is then cut from the tissue block and placed on the tape in association with the markings on the tape (steps 324 and 326), which also correspond to the barcode information on the tissue block. Once the tissue sample is cut from the block, a glass slide is labeled with the same barcode data associated with the tissue block by a just-in-time digital printer (step 328). The tissue section is transported from the microtome to the slide sectioner and placed on a glass slide with printed labeling (step 330). Optionally, a comparison can be made in step 331 between a baseline image of the tissue block and an image of the tissue section. At this point, an error-free association is established between the barcode of the block from which the section was cut and the labeling on the slide containing that section. Finally, the barcode data on the glass slide can be scanned to verify the slide barcode against the block barcode (step 332). In some embodiments, the block face LIMS data, transport medium location markings, and slide barcode data are correlated (step 334) to ensure that the three pieces of information precisely match, thus ensuring tracking of cut tissue samples within the automated tissue sectioning device and ensuring regulatory quality compliance.

[0225] System Implementation

[0226] The quality control analysis described above can be achieved using an automated device for automated transfer of tissue sections from a sample block to a transport medium such as tape, and from the transport medium to a slide. In some embodiments, an automated tape transport system is provided that includes a controller, a support for holding a sample block of tissue to be embedded in an embedding medium, a cutting device configured to cut the tissue section from the sample block, and a transport medium for transporting the cut tissue section from the sample block. The quality control system includes one or more imaging devices configured to take at least a first image of the sample block and at least a second image of the cut tissue section, and the first and second images are compared to confirm that the cut tissue section corresponds to the pre-sectioned tissue of the sample block, e.g., is within preset criteria.

[0227] In some embodiments, an automated method is provided for transporting cut tissue sections from a tissue sample block and providing quality control. The method includes the following steps. a) advancing a transport vehicle in an automated system; b) cutting a first tissue section of the sample block; c) transporting the first tissue section away from the sample block, the cutting exposing a next cut surface of the sample block; d) transferring the first tissue section to a first slide; and e) Comparing the first tissue section to the sample block to determine if a correspondence exists.

[0228] In some embodiments, the automated method includes transporting the cut tissue section to a slide station containing a first slide for transfer to a first slide, and an image of the first cut tissue section is taken on the first slide.

[0229] FIG. 23 provides a workflow diagram for section tracking. In step 340, the workflow involves scanning a tissue block and determining whether the sample block ID is readable using a scanning device (step 342). If not, a determination is made in step 344 whether the block ID is readable by a histotechnician. If not, the block is flagged in step 346; if yes, the block ID is manually typed into the system in step 348. Once the block ID is readable (step 350), either by scanning or manual entry, the tissue is sectioned to create slides as described herein (step 352). If a determination is made (step 354) that the tissue on the slide has blade nicks, air bubbles, missing portions, and / or other unacceptable features as described above, additional sections are cut. If the tissue on the slide is acceptable, a printed indicia for the slide is requested in step 356. In step 358, a determination is made as to the functionality of the slide label printer. If the slide label printer is not functional, the laboratory must implement a process to obtain labels in an alternative manner (step 360). If the printer is functional, in step 362, a label is printed and affixed to the slide. Next, in step 364, the tissue on the slide and the block face are compared (utilizing the methods / processes / systems described herein) to determine if a match exists. If not, in step 366, a determination is made whether any other processed block tissue shapes match the tissue on the slide. If not, in step 368, the slide is flagged, and if yes, in step 370, a check is made to ensure the slide and sample block barcodes match. If not, in step 372, the slide is flagged, and if yes, the slide is acceptable for processing (step 374).

[0230] 24 , the vision system of the present disclosure can be part of an automated microtomy device. In some embodiments, the automated microtomy device 400 can include a combination of mechanisms for receiving a sample block, cutting samples / sections from the sample block, and transferring the samples cut from the block onto a tape to be transferred to slides for analysis. The combination of mechanisms can include at least one microtome 404, a tape transport 406, a slide adhesive coater 412, a slide printer 414, a slide input rack 416, a slide singulator 418 that selects slides from a stack of slides, and a slide output rack 420. This combination of mechanisms works together to prepare the samples on the slides and to prepare the slides themselves.

[0231] FIG. 25 is a schematic diagram of an exemplary embodiment of an automated tape transport device (system) 430 that includes a visualization system having an illumination system and an imaging system. Note that other automated devices may be utilized, and device 430 is shown by way of example. FIG. 25 illustrates the path of a tape 432 for transporting the cut tissue section after the block has been fully sectioned. FIG. 25 shows a microtome 434 used to hold a sample block and cut sections. The microtome 434 holds a sample block with a tissue sample encapsulated within a support block of embedding material, such as paraffin wax. The microtome 434 includes a blade (not shown) that is aligned to cut slices (or sections) from the face of the tissue block.

[0232] In addition to the adhesive tape 432 and microtome 434, the automated tape transport device 430 of FIG. 25 includes a motorized feed mechanism 436, a tape applicator 438, a slide station 440, and a take-up mechanism 442. An illumination system 444 and an imaging system 446 for the block face are shown (schematically) in the drawing. The same or different illumination and imaging systems (not shown) can be utilized for tissue sections on the tape. An illumination system 448 and an imaging system 450 for slides are also shown (schematically) in the drawing. The path of the tape 432 begins at the feed mechanism 436 and progresses toward the microtome 434 and the applicator end of the tape applicator 438. The tape 432 then moves away from the microtome, progresses toward the slide station 440, and is finally stored on the take-up mechanism 442. Note that details of the apparatus / system 430 are described in U.S. Publication Nos. 2017 / 0205317 and 2017 / 0328818, the entire contents of which are incorporated herein by reference. The motorized reel advances the adhesive tape so that the portion of the adhesive tape containing the cut section moves away from the microtome and sample block and a new portion of the adhesive tape is positioned and adhered to the cutting surface for a new section to be cut by the microtome and transferred to the adhesive tape.

[0233] 26 shows the tape applicator as a cycle begins. The tape applicator moves toward the cut surface of the tissue sample block. This causes the roller member of the tape applicator to press the tape, e.g., if adhesive tape is utilized, the adhesive side of the tape onto the cut surface, adhering the tape and covering the entire cut surface with the tape. The tape applicator is then retracted in the opposite direction, resetting the roller member to its original position away from the cut surface. In some embodiments, the cut tissue section is moved into contact with the tape after sectioning by the microtome.

[0234] FIG. 26 shows the slide station 440 of the automated tape transport device 430 in more detail. The slide station 440 may be a UV station for transferring the tissue section on the tape to a microscope slide 460 that is pre-coated with a UV-curable adhesive. A roller may then press the section on the adhesive tape onto the slide. While the system of FIG. 25 includes a slide station for transfer to the slide, it should be understood that in some embodiments, the system does not include a slide station, and after transfer of the cut section to the tape and removal of the tape from the microtome area, the section may be transferred from the tape to the slide according to other methods, such as manual transfer or storage on the tape.

[0235] The slide station 440 has a lower portion 462 with spacers creating a slide slot, a support section 464, a UV source 466, and a motor 468. The slide slot created by the spacers and the support section 464 hold the slide 460. The motor 468 is used to translate or move the lower portion of the slide station 440 to adjust the section location on the slide 460 so that the exact location where the sample section from the tape is deposited on the slide 460 can be controlled. An illumination and imaging system can be provided within or adjacent to the slide station to illuminate and capture images of the tissue section on the slide for quality control, e.g., comparison to a base image of the tissue prior to transfer to tape. The imaging system can also be utilized to assess the condition of the tissue section on the slide for tissue integrity checks. Figure 27 illustrates an exemplary schematic showing the tape 432 prior to application to the surface 470 of a sample block 472.

[0236] As noted above, the illumination and imaging systems disclosed herein can be utilized with other automated equipment, tapes other than adhesive tape, and equipment that does not have an automated slide station, as well as in manual systems.

[0237] The automated system provides for the use of adhesive tape, or alternatively, another transfer medium, to support the sample from the tissue block cut. The automated system and method also provides for automated subsequent transfer of the sample from the adhesive tape to a slide. The system and method further provides improved quality control by providing methods and devices / systems for comparing i) the tissue on the transfer medium and / or ii) the tissue on the glass slide with the tissue on the sample block or slices freshly cut from the block. This is in the context of a fully automated tissue sectioning device, providing automated quality control.

[0238] While the system is described with the use of a continuous strip of adhesive tape, it should be understood that other transport media may be utilized. Adhesive tape, as disclosed herein, adheres to the cutting surface of the sample block prior to sectioning. Following adhesion of the adhesive tape to the cutting surface, the microtome begins the cutting action. The adhesion of the adhesive tape to the cutting surface supports the section being cut by the microtome. Once the microtome completes cutting, the cut section remains adhered to the adhesive tape. In an alternative embodiment, the section can be cut first, followed by adhesion to the transport media.

[0239] It should be noted that tape provides one example of a transport device / system for tissue slices. Other transport systems, such as a robotic arm, a series of cups with water therein, etc., can also be utilized. Tissue in / on these other transport systems can be evaluated according to the quality control system described herein. Thus, the systems described herein, e.g., illumination systems, imaging systems, etc., are fully applicable to slices on a variety of transport systems.

[0240] Due to the tracking of tissue at different stages in the device, e.g., from block to new slice, slice during transport, slice on slide, multiple internal levels of quality control are provided.

[0241] The slides in the slide station can be held stably (firmly) in accordance with some embodiments of the quality control system described herein. In some embodiments, the automated system further includes a support for holding the sample block stably and a support for holding the slide stably in front of one or more imaging devices.

[0242] It should be understood that the term "adhesive tape" as used herein refers to any type of bond, including molecular bonds, mechanical bonds, etc., and may also include dry adhesive tapes that provide bonds via van der Waals (molecular) forces and whose tape peeling force varies significantly depending on the peel angle, minimizing section damage during peeling. The tape can be free of any residue, adhere when needed, and peel off when needed without damaging the tissue. It should also be noted that the term "continuous strip of adhesive tape" as used herein means that the tape is longer than the amount of adhesive tape used for a single section (a single sample of tissue cut from a tissue block). The adhesive area of ​​the adhesive tape can be large enough to completely cover the cut surface of the sample block, i.e., to hold the complete section when it is sliced ​​from the sample block.

[0243] An example of an automated device is illustrated in FIG. 26, described above, and further described in commonly assigned U.S. Publication No. 2017 / 0205317. Other examples of automated devices and variations thereof are disclosed in U.S. Publication Nos. 2017 / 0003309 and 2017 / 0328818, the entire contents of which are incorporated herein by reference. It should be understood that the illumination / imaging system and quality control system can be used in conjunction with other automated devices, and therefore these automated devices provide examples of automated devices. Also, as discussed herein, the illumination / imaging system and section tracking and quality control system can be used in conjunction with manual systems and methods.

[0244] The automated tape transport device may include a programmable digital controller, processor, or other type of application-specific integrated circuit (ASIC) used to control the movements of the automated tape transport device 1, communicate with a user of the automated tape transport device 1, and / or communicate with the microtome 4 to which the automated tape transport device 1 is connected. There are many movements that can be controlled within the automated tape transport device 1. Examples of these movements include movement of the feed mechanism 3 and take-up mechanism 6, movement of the lower portion 30 and translation portion of the slide station 5, movement of the linear actuator member, etc. The controller may also provide information to the user regarding the function or condition of the automated tape transport device 1, such as the number of slides prepared, the number of sections transported, the amount of tape remaining on the roll, etc. The controller can receive any type of input (e.g., mechanical, visual, electrical, etc.) to perform its control functions. The controller, in some embodiments, can also control the quality control system described herein.

[0245] In some embodiments, the automated tape transport apparatus 1 further includes an optical device for inspecting the sample block. For example, the microtome 4 may store multiple sample blocks for sectioning. The optical device may be used to assess the condition of the section surface or to determine the location of the tissue within the embedding medium. In one example, a macroscopic image of the section surface may enable more precise placement of the adhesive tape 2 on the section surface. Analysis of the section surface may facilitate automatic trimming of the section surface to expose the desired tissue for sectioning.

[0246] In some embodiments, one or more optical sensors may be used to provide feedback to the controller regarding the location and quality of the slices on the adhesive tape 2. For example, a brightness sensor in close proximity to a backlit section of the adhesive tape 2 may distinguish between empty portions of the adhesive tape 2 and portions carrying slices. This may provide the approximate location of the slices on the adhesive tape 2, which may be used as an input to the controller for various purposes, such as motion control. A CCD imager or similar device may be used to image the slices and provide feedback regarding the quality of transfer. These images may be used to check for errors in the process, such as incomplete transfer of the slice, misalignment of the slices on the adhesive tape 2, or the presence of slice trimming waste on the tape. In the event of these errors, additional slices may be taken to replace the defective slices.

[0247] Similar optical methods of inspecting sections on slides may also be used. A sensor system may provide feedback on the quality of section transfer to the slide and alert the controller to errors in the process. The same or different optical sensors may be used for inspection of both the tape and the slide.

[0248] The automated tape transport device, in some embodiments, may also include an automated system for labeling slides and sample blocks with barcodes or other monikers for identification. Possible slide labeling methods include attaching adhesive printed labels, etching labels into materials, or printing labels on dedicated locations. The labels may link the slide to associated information, such as the tissue block of origin and the sectioning date. Sample blocks may be similarly labeled. To accommodate pre-labeled blocks, an optical reader, such as a barcode reader, may be used to read the block labels and generate the associated slide labels.

[0249] The system may also include an automated quality control system for comparison of the cut tissue with the tissue on the sample block to ensure that the cut tissue is properly labeled on the slide to match the sample block.

[0250] It should be noted that the use herein of the terms tissue section or cut section contemplates that the initial sections cut from the sample block may not contain much tissue because they may contain overlying material, such as paraffin or other embedding medium. However, what is important for histopathology is the tissue section, i.e., the area of ​​the tape that contains enough tissue section that these are the ones selected for transfer to the slide. Features to ensure this can be provided in the manner described herein.

[0251] The tape transport system can include one or more automated imaging devices, such as a digital camera, for taking photographs during various stages of the automated tape feeding / advancement process. Photographs can be taken at the time of cut section transfer to the tape, at the time of cut section transfer to the slide, and / or at any other time during the process. Such photographs can provide visual / quality control as described herein.

[0252] A photograph of the sample block (block face) can also be taken. For example, a discrepancy between the block face image and the section image on the tape is a clue as to an error during sectioning. A macro image can be useful in thumbnails in a database listing the section images. This can be useful to roughly determine when to begin transferring the section to the tape when cutting. There are various ways to image tissue in the system other than a digital camera. For example, micro-CT can be used to build a 3D model of the tissue in the paraffin. If the system has a 3D model of the tissue in the block as input, it can use the information to determine when to stop trimming and sectioning.

[0253] In another aspect of visual / quality control, as the tape advances through the apparatus and sections are cut from the sample block by the microtome and adhered to the tape adhesive, a photograph (or other imaging technique) of each tape area containing a tissue sample (cut section) being transferred to the adhesive tape is taken, thereby allowing real-time analysis to ensure that the section has been properly, i.e., completely, transferred to the tape. Utilizing the same camera or imaging device, or alternatively, a separate camera or imaging device, the tape with the adhered sections cut from the sample block advances to the slide station, and as the sections are transferred to the slides, a photograph (or other imaging technique) of each slide containing the sample is taken, allowing real-time analysis to ensure that the section has been properly, i.e., completely, transferred to the slide. In this way, the process can be monitored to ensure that the proper sections of the sample block are cut and transferred to slides for pathology before tape advancement is stopped. In some embodiments, if an incorrect section is being transferred, the system is reversed and the tape is rewound in the opposite direction to the initial advance, allowing more sections (samples) to be collected and transferred from the sample block. Also, note that multiple photographs of each tape area and each slide containing cut sections can be taken for evaluation. The lighting and imaging systems described herein enhance this analysis.

[0254] Other information from the photographs can also be stored to identify sample blocks, sections, etc., along with marking and tracking of the blocks and sections.

[0255] In a visual control system implementation, a photograph is taken of each tape area containing a section, e.g., a tissue section, cut from the sample block by the microtome. The photograph is then analyzed to determine whether the cut section has been properly transferred to the tape. In a further analysis, the photograph is evaluated to determine completion of sample block trimming (described below). Once the tissue section is transferred to a slide in the slide station (downstream of the microtome), an image of the slide is also taken. This photograph of the slide is analyzed to determine whether the tissue section has been properly transferred to the slide. The photograph can also be analyzed to determine whether a sufficient tissue section is contained on the slide. The photograph can also be used for matching to the sample block. If a section is not sufficient, for example, it does not contain enough tissue sample as a result of, for example, it containing a large amount of paraffin, the section is not used for evaluation. The illumination and imaging systems described herein enhance these analyses. The illumination and imaging systems described herein enhance these analyses.

[0256] The photographs can be stored in a database for future selection if further use and analysis is desired.

[0257] 28A, 28B, 28C, 29, and 34 illustrate exemplary embodiments of automated systems for implementing the methods described above. However, it should be noted that the methods and systems described above can be implemented in manual or other automated microtomy processes.

[0258] 28A and 28B, in some embodiments, an automated system 500 is provided to enable automated tissue sample processing from block to slide. The system 500 can be designed to include a first section for cutting samples from tissue blocks. In some embodiments, the first section, as shown in FIG. 28B, for example, can include a block handler, at least one microtome 504, a transport medium 506 (e.g., tape), a hydration chamber 508, and a block tray 510. The block handler, at least one microtome 504, the transport medium 506 (e.g., tape), the hydration chamber 508, and the block tray can be designed to work together to organize, section, hydrate, and slice biological samples from tissue blocks, and transfer the tissue sections to slides using any combination of systems and methods.

[0259] In some embodiments, the system 500 can include a transport medium 506 (e.g., tape) for receiving sample slices taken from a tissue block, for example, by the sectioning microtome 504. The transport medium 506 can include any combination of materials or surfaces capable of receiving a sectioned sample from the microtome 504 and transporting the sectioned sample to another location. In some embodiments, the transport medium 506 can include at least one adhesive surface capable of removing, receiving, and / or transporting a sectioned sample from the microtome 504 after it has been cut from the tissue block. For example, the transport medium 506 can include any combination of tapes, such as, for example, a tape roll, windowed tape, etc. The transport medium 506 can include, or otherwise be a part of, a larger mechanism for transporting the sectioned sample. For example, the transport medium 506 can be an adhesive tape wrapped around a combination of pulleys, wheels, spools, conveyors, etc., designed to allow the transport medium 506 to move the sectioned sample thereon from one location to another. Any other combination of transport media can be used without departing from this disclosure. For example, transport media 506 can be a belt with ridges, depressions, etc. designed to grip and / or hold the sectioned sample.

[0260] In some embodiments, the transfer medium 506 can transfer the sectioned sample from its surface to the shift assembly 522 for transfer of the sample onto a slide. The shift assembly 522 can be designed to remove the sample adhered to the transfer medium 506 and place the sample on one or more slides. In some embodiments, the transfer by the shift assembly 522 can include separating the actual tissue sample material to isolate the sample from non-sample material. The shift assembly 522 can use any combination of systems and methods for separating all or part of the biological sample relative to the surrounding paraffin material so that only the biological sample material is transferred to the slide. For example, the shift assembly 522 can center the portion of the biological sample to be removed from the transfer medium 506. In some embodiments, the non-sample material (e.g., paraffin material) can remain on the transfer medium 506 to be discarded with the used transfer medium 106.

[0261] Continuing with FIGS. 28A-28C, system 500 can also include a second section, as shown in FIG. 28C, having a combination of mechanisms for preparing and providing slides for receiving biological samples cut from blocks (e.g., in the first section) from a transport medium 506 (e.g., tape) and for processing the slides for analysis. In some embodiments, the combination of mechanisms for processing slides in the second section can include a slide adhesive coater 512, a slide printer 514, a slide input rack 516, a slide singulator 518, and a slide output rack 520. This combination of mechanisms can function together to prepare slides for receiving samples, adhere the samples onto the slides, and deliver / organize the slides with the samples into a rack for later use. In some embodiments, initial blank slides can be provided in a storage rack of the slide assembly for pre-processing. For example, the slide assembly can include one or more slide input racks 516 for storing multiple blank slides. The slide assembly can store and organize a large capacity of slides, e.g., 200 slides.

[0262] In some embodiments, the slide singulator 518 can be designed to grab a slide from a stack of slides in the input rack 116. The slide singulator 518 can include any combination of mechanisms capable of picking up and transporting slides. For example, the slide singulator 518 can be an actuated mechanical arm, a gantry, etc. Before being processed, the slide singulator 518 can provide the slide for a quality control step. During the quality control step, analysis can be performed on the slide to ensure that the slide is suitable for receiving a sample. For example, quality control can include the slide singulator 518 transporting the slide within the field of view of a camera to identify any potential problems with the slide and provide image data for image processing to check slide orientation, slide condition, etc. If the slide fails the quality control inspection, it can be discarded; if it passes, it can be transported within the system 500 and prepared to receive a sample. In some embodiments, the slide can be transported to the slide printer 514 to receive identification information printed thereon. For example, information about sample type, sample origin, sample date, etc. can be printed on the slide. The identification information can include any combination of machine-readable and human-readable codes or text such that the slide and its contents can be properly identified and tracked. For example, the slide printer 514 can print a machine-readable barcode on the slide to identify the slide number, batch, contents, etc.

[0263] In some embodiments, slides can be transported to slide adhesive coater 512 to be coated with an adhesive material. For example, slide adhesive coater 512 can spray ultraviolet (UV)-activated adhesive onto the slides, apply UV-activated adhesive tape, or any combination of adhesive systems or methods. In some embodiments, the adhesive can be applied in multiple layers. Multiple layers can be applied to ensure that the slides receive a uniform coating of adhesive and clear visibility through the slide layers. In some embodiments, slides can be inserted into slide input rack 516 already pre-processed or partially pre-processed.

[0264] Once the slide has been processed by the slide printer 514 and slide adhesive coater 512, the slide can be transported to the transport medium 106 to receive the sample from the transport medium 506. For example, the slide can be transported to the shifting assembly 522 to receive the sectioned tissue block sample from the transport medium 506 (e.g., a tape mechanism). In some embodiments, prior to transferring the sample to the slide, the shifting assembly 522 can include one or more cameras and perform image processing to determine whether the sample in the transport medium 506 is suitable for adhesion to the slide. For example, the image processing can inspect the sample to determine whether it is suitable for placement on the slide. If it is not suitable, the sample can be discarded and the transport medium 506 can be advanced to the next sample. When the sample is suitable for placement on the slide, it can be applied to the slide. In some embodiments, the image processing can inspect the sample after it has been adhered to the slide to determine whether the placement of the sample is of sufficient quality. For example, image processing can inspect the slide to determine whether the sample is cleanly adhered to the slide, whether there are any air bubbles, tears, residual paraffin, etc. If the slide is not suitable, the slide can be discarded instead of being placed in the slide output rack 520.

[0265] In some embodiments, the completed slides can be transported by singulator 518 to be stored in slide output rack 520. The slides can be stored in slide output rack 520 in a predetermined order and / or organized manner so that the next step in which the slides will be used can easily locate and remove the slides.

[0266] As noted above, in some embodiments, the system 500 may include a quality control imaging system, such as that disclosed in co-pending U.S. Application No. 62 / 980,203, filed February 22, 2020 (which is incorporated by reference in its entirety herein).

[0267] Referring to FIG. 29 , in some embodiments, system 500 can be used to transfer samples from tissue blocks to slides according to steps provided in an automated process flow 600. FIG. 29 shows the process flow of the block-to-slide steps used in system 500 provided in FIGS. 28A-28C . In step 601, a sample tissue block can be loaded into system 500. For example, one or more tissue blocks with tissue samples embedded in paraffin blocks can be loaded into tray 510 and placed in system 500. In step 602, one of the sample tissue blocks can be moved from tray 510 to microtome 504 for sectioning. For example, the tissue block can be transported by a handler and placed in the chuck of sectioning microtome 504 to be sectioned. In step 603, the sectioned tissue block can be moved to hydration chamber 508 for hydration and cooling. For example, a tissue block can be transported by a handler and placed in hydration chamber 508 for a predetermined period of time. After sufficient hydration is provided, the tissue block can be moved to microtome 504 for sectioning in step 604. For example, a tissue block can be transported by a handler and placed in the chuck of sectioning microtome 504 for polishing and sectioning. The block can be provided to the same microtome 104 where the sectioning was performed or to a different microtome 504. Each sectioned sample can then be transferred to transport medium 506. In step 605, the sectioned samples on transport medium 506 can be transferred to slides.

[0268] Concurrently with or subsequent to steps 601-605, steps 606-608 can be performed to prepare one or more slides for combination with sectioned samples from the tissue block. In step 606, a microscope slide can be selected and retrieved from a stack of new slides. For example, slide singulator 518 can select and pull a slide from a stack of slides stored in blank slide rack 516. In step 607, identification information can be printed on the selected slide. For example, the slide can be placed in slide printer 514 to have a machine-readable barcode printed thereon. In step 608, an adhesive material can be coated on the selected slide. For example, the slide can be placed in slide adhesive coater 512 to have a UV-activated adhesive sprayed thereon. In step 609, a tissue sample can be transferred from transport medium 506 to the UV-adhesive-coated slide. Additionally, during step 609, the slide can be imaged for on-board diagnostics, quality control, and sample tracking. For example, one or more cameras can be used to capture image data to be processed by an image processor with respect to a predetermined quality threshold. Once the slide passes quality control, in step 610, the completed histology slide can be moved to an output rack 520 to be stored for future analysis.

[0269] algorithm

[0270] The flowchart in FIG. 30 illustrates the steps of a motor-controlled automated system for transferring tissue sections cut by a microtome to tape and further transferring the tissue sections to slides. For example, the automated system can include a removable tape or other support / transport medium, and the tissue sections are automatically transferred to the tape by the device. Once the system, the imaging system, determines that the block is fully sectioned as described above so that the tissue sections can be transferred to tape for subsequent analysis, a feeding mechanism is automatically activated (or alternatively, the device can be designed so that the user will activate the feeding mechanism once the block is fully sectioned). Activation of the feeding mechanism advances the tape, which is moved toward the cutting surface of the sample block as described above. Next, a roller, e.g., a roller member, presses the adhesive side of the tape, e.g., adhesive tape, onto the cutting surface. The roller is then pressed down so that the tape covers the entire cutting surface. The linear actuator is retracted to its original position to reset the roller for subsequent application of tape to the block for transfer of another cut section. The microtome then cuts the section covered by the tape (e.g., along a plane parallel or nearly parallel to the cutting surface). The cut section carried by the tape is advanced to the slide station and aligned with the slide. After the cut section of tissue is transferred to the tape by the automated device, the tissue section is subsequently transported by the automated device to a glass slide at the slide station and automatically transferred to the glass slide. The slide roller presses the section on the tape onto the slide, allowing the section to be stacked on the slide. The slide roller is retracted to its original position, and the tape is advanced away from the slide, leaving the section on the slide. These steps in Figure 30 are repeated until the desired number of sample sections have been transferred to the tape, cut by the microtome, and transferred to slides.

[0271] As shown in FIG. 30 , the feed mechanism is activated to advance the tape in step 700. Next, the linear actuator moves toward the cutting surface of the sample block in step 702. A roller member presses the adhesive side of the tape onto the cutting surface in step 704. The roller member is then depressed to adhere the adhesive tape to cover the entire cutting surface in step 706. The linear actuator retracts in step 708 to reset the roller member for subsequent application of adhesive. The microtome cuts the section covered by the adhesive tape in step 710, and the cut section advances to the slide station and aligns with the slide in step 712. Slide rollers press the section onto the slide in step 714, and the section is laminated onto the slide in step 716. Optionally, a comparison can be made in step 717 between a baseline image of the tissue block and an image of the tissue section on the slide to ensure a match between the tissue block and the tissue section. The slide roller retracts to its original position in step 718. Finally, the tape advances away from the slide in step 720 and is stored on the take-up mechanism.

[0272] In some embodiments, a quality control system can be provided for equipment or component checks of the automated system. More specifically, software algorithms can be utilized to determine whether the tissue transport system is functioning according to manufacturing specifications based on variations in tissue images and projection patterns. This can be based, for example, on images of tissue on the tape. In an alternative variation, landmark features of fixed mechanical components can be used as references instead of projection patterns to determine tissue orientation variations. Such features can be useful for predictive maintenance of the device. If everything is functioning according to specifications, the tissue will be transferred to the tape in the same nominal location. If the tissue transfer is in a sufficiently different location, this can alert the user that the mechanical components are misaligned or not functioning properly. For example, if a different location is detected, this can mean that the rollers need to be aligned, the tape tension needs to be the same between transfers, e.g., a tension sensor is out of alignment or the sensor is operating at a different point, the applicator tension spring from the tape to the block still does not have the specified spring constant, the tape used for transfer does not have the same elastic constant and specified one, etc. It should be understood that no single metric can point to any individual reason, but it may alert the technician that there is a problem in the tissue transfer line that needs to be corrected. However, it is also envisioned that the system may provide algorithms that can more specifically detect the source of the mismatch, and thus identify the machine component requiring adjustment.

[0273] The tissue imaging system is shown in conjunction with the tape transport apparatus (system) of FIG. 25 , along with the flowchart of FIG. 31 , which illustrates the steps of an automated tape transport system. Note that a single imaging device, e.g., a digital camera, can be utilized to take photographs adjacent the transfer of the cut sections to the tape adhesive. The same camera can be repositioned adjacent the slide station during automated operation to take photographs of the slides after the sections are transferred to the slides. Alternatively, a different imaging device can be provided within or adjacent to the slide station to take photographs after the sections are transferred to the slides. As noted above, the apparatus of FIG. 25 can take photographs of the cut sections after transfer to the tape and from the tape to the slides, or alternatively, take photographs only after transfer to the tape or only after transfer to the slides. Such photographs can be taken at the time of transfer, immediately after transfer, or downstream of transfer (after the tape has advanced past the tape applicator or to the slide station). Photographs of the tape and / or cut sections of the tape can also be taken at other times during the tape feeding cycle if desired.

[0274] First, the feed mechanism is activated to advance the tape in step 730. A linear actuator moves toward the cutting surface of the sample block in step 732. A roller member presses the adhesive side of the tape onto the cutting surface in step 734, and the roller member is depressed to adhere the adhesive tape to cover the entire cutting surface in step 736. The linear actuator retracts to reset the roller member for subsequent application of adhesive in step 738. The microtome cuts the section covered by the adhesive tape in step 740. A photograph of the tape-covered cut section is taken in step 742, and the cut section is advanced to the slide section and aligned with the slide in step 744. Next, a determination of tissue sufficiency is made in step 746. If there is not enough tissue section for transfer onto the slide, the section is not transferred to the slide and remains on the tape in step 748. The tape is then advanced away from the slide and stored on the take-up mechanism in step 758. When the tissue section is sufficient for transfer onto the slide, the slide roller presses the section onto the slide in step 750, the section is laminated onto the slide in step 752, and a photograph of the section on the slide is taken in step 754. Finally, the slide roller retracts to its original position in step 756, and the tape is advanced away from the slide and stored on the take-up mechanism in step 758.

[0275] Referring to the flowchart of FIG. 31 , after a tape, e.g., a tape cartridge, is loaded onto the feed mechanism, the feed mechanism 436 is activated to advance the tape, i.e., a continuous length of adhesive tape. A linear actuator member 438 is moved toward the cutting surface of the sample block. Next, a roller member presses the adhesive side of the tape onto the cutting surface. The roller member is then depressed to adhere the adhesive tape to cover the entire cutting surface. The linear actuator 438 is retracted to its original position to reset the roller for subsequent application of adhesive tape to another sample. The microtome then cuts a section (along a plane parallel or nearly parallel to the cutting surface) covered by the adhesive tape. A photograph of the cut section is taken by a digital camera either at the time of transfer or immediately after transfer. The photograph is analyzed to confirm proper transfer to the tape. The cut section is advanced downstream to the slide station 440 and aligned with a slide. At this point, the photograph is analyzed to determine whether a sufficient section of tissue has been cut from the sample block for transfer to a slide. If the section is not sufficient, for example, it does not contain enough tissue sample as a result of, for example, it containing mostly paraffin, the section is not transferred to the slide and remains on the tape. If the tape area contains sufficient tissue section, it is ready for transfer to the slide, and the slide rollers press the section onto the slide, and the section is then laminated onto the slide by the various methods described above. A photograph of the cut section and slide is taken at the time of transfer to the slide or immediately after transfer. Note that the photograph can be taken before or after lamination onto the slide. Note that the slide from the slide machine will have a barcode or other identification system that corresponds to the barcode or other identifier on the sample block. The slide rollers are retracted to their original position, and the tape is advanced away from the slide and stored on the take-up reel of a tape cartridge mounted on a take-up mechanism. These steps in Figure 31 are repeated until the desired number of sections from the sample block have been cut by the microtome, transferred to tape, and transferred to slides.Photographs of each of these sections are taken as they are transferred to tape and as they are transferred to slides for analysis during the tape feed operation (quality control).

[0276] The flowchart of Figure 32 is for a system similar to that of Figure 31, except that the sample tape is removed from the carrier strip, as in the system of U.S. Publication No. 2017 / 0003309. Analysis of photographs according to the flowcharts of Figures 31 and 32 is enhanced by the use of the lighting and visioning system described herein.

[0277] As shown in FIG. 32 , a feed mechanism is activated to advance a carrier strip carrying a patch of sample tape with adhesive in step 760. The sample tape is then aligned with the sample surface in step 762. In step 764, rollers move to press the sample tape onto the sample surface, with the carrier strip guides now in the application position. The rollers retract to their initial positions in step 766. In step 768, the carrier strip guides move to the removal position, moving the carrier strip out of the path so that it separates from the sample tape. The microtome cuts a section of the sample in step 770, and a photograph of the cut section on the tape is taken in step 772. The sample tape with the attached section is then advanced to the slide station and aligned with the slide in step 774. A determination of tissue sufficiency is then made in step 776. If the tissue section is not sufficient for transfer onto the slide, the section remains on the sample tape rather than being transferred to the slide in step 778. If the tissue section is sufficient for transfer onto the slide, the slide roller presses the section onto the slide in step 780, the sample tape is removed in step 782, and the section is laminated onto the slide in step 784. Finally, a photograph of the section on the slide is taken in step 786.

[0278] As discussed above, the automated system has an image-based quality control system for comparing tissue on the block face of a sample block with tissue sections transferred to glass slides. One or more imaging devices acquire digital images of the block face, and one or more imaging devices acquire digital images of the tissue sections on the slides onto which the tissue sections are transferred and retained, and the images of the sample block and slide are compared to ensure a match. That is, images from the sample block and images from the slides containing the tissue sections are compared to determine whether a match exists or does not exist. This provides a backup system to the barcodes provided on the cassettes carrying the tissue blocks and on the slides. In this way, if a barcode match is confirmed, a double check is performed by the automated device through image comparison. Therefore, quality control does not rely on human assessment.

[0279] To achieve such quality control, some embodiments provide three features: 1) a series of image capture devices positioned to capture the desired tissue images, 2) contrast is created to improve differentiation between tissue and paraffin (or other embedding medium) on the digital image and facilitate comparison / analysis, and 3) tissue blocks and slides are held stably (rigidly) to minimize, or in some embodiments, completely prevent, block and slide movement, enhancing imaging. Each of these features is discussed below.

[0280] The automated system can include a computer system for collecting images from the block-facing camera and the slide-facing camera, along with software for comparing images from the block face and slide. A software algorithm determines the tissue contours from each image and compares the two images. Images can be stored for later comparison, if desired.

[0281] The computer system can have a decision algorithm for determining whether the images from the block face and slide match. The decision algorithm has knowledge of the identities of the sample block and glass slide from which the images were captured. The decision algorithm verifies that the sample also has a matching identity. Matching identity can involve matching tissue contours as described herein. Matching identity can also involve matching barcodes on the sample block and slide, for example, as shown in Figures 17A and 17B described herein.

[0282] Various types of imaging devices can be provided. It should be noted that the terms “imaging device” and “image capture device” are used interchangeably herein and will be discussed and illustrated in terms of a digital camera for convenience; however, it should be understood that various devices and methods for capturing images are also contemplated, including, for example, X-ray, infrared, tomography, micro-CT imaging, OCT cameras, etc. A single imaging device can be provided, but alternatively, multiple imaging devices are provided adjacent to the sample block and adjacent to the slide that receives the tissue section to enhance the image. It should be noted that the image capture device, e.g., a digital imaging device such as a digital camera, can have an optical filter for incident light as the image capture device acquires the image of the block to enhance clarity.

[0283] The imaging system may include a box containing the object to be imaged and imaging hardware to prevent stray light from being captured by the camera.

[0284] In some embodiments, another aspect to having clear, high-contrast images is minimizing vibration between the image capture device and the object. The automated system can include a mechanism for stably holding a sample block of tissue to be sectioned in front of multiple cameras. This enhances images when using vibration-sensitive cameras by reducing sample block vibration, as such vibrations reduce the performance of image post-processing tools by blurring images and making tissue comparison more difficult. The sample block is held in place using a servo motor that monitors the sample's position in real time. In one embodiment, the sample block is held in place using a high-inertia mounting bracket attached to the same reference frame as the image capture device. Other mechanisms for stably holding the sample block are also contemplated.

[0285] Similarly, vibration between the image capture device and the slide is minimized to provide a "second" image, i.e., a clear, high-contrast image of the cut tissue section on the slide. Thus, similar to stably holding a sample block as discussed above, the automated system can include a mechanism for stably (rigidly) holding a slide containing a cut tissue sample in front of multiple cameras. This stable holding enhances the image by reducing slide vibration, as such vibration reduces the performance of image post-processing tools by blurring the image and making tissue comparison more difficult. The slide can be held rigidly in place within the slide station by a slide holder during imaging. Alternatively, a mechanism such as a mounting bracket can be incorporated as part of the slide station.

[0286] The system and method of one embodiment of the automated system will now be described in conjunction with the flowchart of FIG. 33. The described method is an automated biological tissue sectioning device that processes paraffin-embedded biological tissue and produces thin sections on glass substrates. The thin sections are suitable for analysis under a microscope after further processing. In the method, the tissue shape on the block face is compared to the tissue contour on a glass slide. This is done in the context of a fully automated tissue sectioning device, providing automated quality control capabilities. Thus, the system provides input and output product comparison for the automated biological tissue sectioning device, thereby providing quality control of the biological tissue being cut and mounted on the glass slide.

[0287] As shown in FIG. 33 , a photograph of the sample block is taken in step 790, and a feed mechanism is activated to advance the tape in step 792. A linear actuator moves toward the cutting surface of the sample block in step 794. Next, a roller member presses the adhesive side of the tape onto the cutting surface in step 796. The roller member is then depressed to adhere the adhesive tape to cover the entire cutting surface in step 798. The linear actuator retracts in step 800 to reset the roller member for subsequent application of adhesive. A microtome cuts the section covered by the adhesive tape in step 802, and a slide roller presses the section onto a slide in step 804, and the section is laminated onto the slide in step 806. An image of the section on the slide is taken in step 808. The slide roller retracts to its original position in step 810 and the tape advances away from the slide for storage on the take-up mechanism in step 812. The section image is compared to the sample block image to confirm a match in step 814. Optionally, a comparison can be made between a baseline image of the tissue block and the section image in step 815 to ensure a match between the tissue block and the tissue section. The barcode on the slide is compared to the barcode on the sample block to confirm a match in step 816.

[0288] More specifically, with reference to the flowchart of FIG. 31 , the steps are similar to the system described in conjunction with the flowchart of FIG. 31 , except for the addition of quality control. The system of FIG. 31 also does not have a quality control step that determines whether the tissue should be transferred to a slide; however, a quality control system can be used in conjunction with a system that performs such a step. In the initial step of FIG. 31 , one or more photographs of the sample block are taken with a digital camera. The initial photographs can be taken before or after activation of the feeding mechanism. The images are stored for comparison with images taken later in the process, i.e., after transfer to a slide (or transfer to a tape). Next, the method includes the steps of moving a tape toward the cutting surface of the sample block, pressing an adhesive tape onto the cutting surface to adhere the cutting surface to the surface (e.g., the entire surface of the cutting surface), cutting the tissue section via a microtome, advancing the cut tissue section on the tape to a slide station, pressing the tape section onto the slide, and stacking the section on the slide. In accordance with the quality control system, an image of the tissue section on the slide (before or after lamination) is taken by a digital camera. The sectioned image is compared to the sample block image to confirm a match. The barcode on the slide is also compared to the barcode on the sample block to confirm a match. This section comparison between the sample block and the tissue section on the slide is shown in FIG. 17A, where a captured image of the top of the sample block containing the tissue embedded in paraffin is compared to the tissue section on the slide. The barcode on each slide is compared to the barcode on the back of the sample block, as shown in FIG. 17B, which illustrates a slide and paraffin block identification comparison. Note that the barcode comparison can be performed before or after the tissue image comparison.

[0289] It should be noted that the steps in the flowchart provide one embodiment for use of the quality control system, and it is understood that the steps do not have to be performed in the strict order of the blocks in FIG.

[0290] It should be understood that the quality control system described in conjunction with the method of Figure 33 may include a quality control system that takes a photograph of the tape as the tissue section is transferred to it. A quality control system for identification matching for positive verification can also be used without this tape section transfer photo check. An identification matching quality control system can be used in conjunction with any of the devices / systems and methods described herein.

[0291] It should be understood that a single camera or multiple cameras (or other imaging devices) may be used for the sample block, section, and / or slide images, and / or tape images. Additionally, it is also contemplated that a single camera (or other imaging device), either stationary or mobile, may be utilized to capture images of the sample block, tape, and / or slide.

[0292] Note that multiple images of the sample block can be taken to provide a one-to-one comparison of the image of each slide. For example, before each section is cut, an image of the block face can be taken for comparison with the slide containing that particular cut section. Alternatively, only a single base image or a few base images of the sample block can be taken for comparison with the image of each slide.

[0293] According to another aspect of the quality control system, images of slides are processed to check for air bubbles or tears, i.e., to look for artifacts to confirm proper transfer of the cut tissue section to the slide. If air bubbles are present, the slide can be discarded. In a second level of such an artifact quality control system, if an artifact is detected, the system would then determine whether the artifact is on the tissue or the paraffin. If on the tissue, the slide can be discarded; if on the paraffin, the slide can still be used, as this will not affect the tissue analysis. This artifact quality control system can, in some embodiments, be utilized in addition to the sample block / slide image comparison quality control system described herein.

[0294] As noted above, various embodiments disclosed herein contemplate that, in some applications, multiple sections may be transferred to a single slide. It is also contemplated that, in some embodiments, not all of the sections (or slides) will be stained. For genetic analysis, tumor-specific sections of tissue are typically performed on blank or unstained sections to preserve DNA, because staining can destroy DNA. However, because unstained sections are primarily transparent under the microscope, the contrast between normal tissue and tumor tissue is very poor. In the systems disclosed herein, the slide station can, in some embodiments, include alternating stained and unstained slides. That is, by placing an unstained section (slide) adjacent to a stained section (slide) and detecting the positioning of the section (and therefore the slide) on the tape using the tracking methods disclosed herein, the unstained slide can be genetically analyzed. Thus, a stained slide that is approximately identical to the unstained slide will provide the area / coordinates for collecting material from the unstained slide. This is achievable because the cut sections are typically 5 microns thick, which is approximately half the size of a cell.

[0295] As described herein, photographs are taken at various stages of the tape feeding cycle for real-time analysis. Such photographs can be utilized in addition to, or as an alternative to, the optical sensors discussed above to provide feedback on the quality of the sections transferred to the tape and / or the quality of the sections transferred to the slides.

[0296] Any collected images and barcode associations can, in some embodiments, be synchronized with a Laboratory Information Management System (LIMS). As images / spectra are acquired or decisions are made, these images / spectra / decisions can enter the LIMS. Thus, the quality control system disclosed herein can facilitate such integration.

[0297] The automated system can include a computer system for collecting and analyzing the imaging data collected by the imaging system 2. The images can be stored for later analysis or comparison, if desired. The computer system can have a decision algorithm for determining (in a binary analysis) whether the images from the block face, tape, or slide indicate a tissue abnormality.

[0298] Any suitable computing system can be used to implement the computing devices and methods / functionality described herein and, as will be understood by those skilled in the art, can be converted into a specific system for performing the operations and features described herein through hardware, software, and hardware modifications in a manner that goes significantly beyond simply running software on a general-purpose computing device. An illustrative example of such a computing device 900 is depicted in FIG. 34. Computing device 900 is merely an illustrative example of a suitable computing environment and does not limit the scope of the present invention in any way. A "computing device" as represented by FIG. 34 can include a "workstation," a "server," a "laptop," a "desktop," a "handheld device," a "mobile device," a "tablet computer," or other computing device, as will be understood by those skilled in the art. Given that computing device 900 is depicted for illustrative purposes, embodiments of the present invention may utilize any number of computing devices 900 in any number of different ways to implement a single embodiment of the present invention. Thus, embodiments of the present invention are not limited to a single computing device 900 or to a single type of implementation or configuration of an exemplary computing device 900, as will be understood by those skilled in the art.

[0299] Computing device 900 may include a bus 910 that may be coupled, directly or indirectly, to one or more of the following illustrative components: memory 912, one or more processors 914, one or more presentation components 916, input / output ports 918, input / output components 920, and power supply 924. Those skilled in the art will appreciate that bus 910 may include one or more buses, such as an address bus, a data bus, or any combination thereof. Those skilled in the art will additionally appreciate that, depending on the intended application and use of a particular embodiment, multiple of these components may be implemented by a single device. Similarly, in some cases, a single component may be implemented by multiple devices. Thus, FIG. 34 is merely an illustration of an exemplary computing device that may be used to implement one or more embodiments of the present invention and does not limit the invention in any way.

[0300] Computing device 900 may include or interact with a variety of computer-readable media. For example, computer-readable media may include random access memory (RAM), read-only memory (ROM), electronically erasable programmable read-only memory (EEPROM), flash memory or other memory technology, CD-ROM, digital versatile disk (DVD), or other optical or holographic media, magnetic cassettes, magnetic tape, magnetic disk storage, or other magnetic storage devices that may be used to encode information and that may be accessed by computing device 900.

[0301] The memory 912 may include computer storage media in the form of volatile and / or nonvolatile memory. The memory 912 may be removable, non-removable, or any combination thereof. Exemplary hardware devices are devices such as hard drives, solid-state memory, optical disk drives, and the like. The computing device 900 may include one or more processors that read data from components such as the memory 912, various I / O components 920, and the like. The presentation component 916 presents an indication of the data to a user or other device. Exemplary presentation components include a display device, a speaker, a printing component, a vibrating component, and the like.

[0302] The I / O ports 918 may allow the computing device 800 to be logically coupled to other devices, such as I / O components 920, some of which may be built into the computing device 900. Examples of such I / O components 920 include a microphone, a joystick, a recording device, a gamepad, a satellite dish, a printer, a wireless device, a networking device, and the like.

[0303] While the above description contains many specifics, those specifics should not be construed as limitations on the scope of the disclosure, but merely as exemplifications of preferred embodiments thereof. Those skilled in the art will envision many other possible variations that are within the scope and spirit of the disclosure.

Claims

1. A method for quality control in a histology system, comprising: receiving a tissue block comprising a tissue sample embedded within an embedding material; imaging the tissue block to generate first imaging data of the tissue sample in a tissue section on the tissue block; removing the tissue section from the tissue block, the tissue section comprising a portion of the tissue sample; imaging the tissue section to generate second imaging data of the tissue sample in the tissue section; comparing the first imaging data with the second imaging data and confirming correspondence of the tissue samples in the first imaging data and the second imaging data based on one or more quality control parameters; A method comprising:

2. The method described in claim 1, wherein the tissue section is unsuitable if there is no correspondence of one or more quality control parameters in the tissue sample in the first imaging data and the second imaging data.

3. The method of claim 2, wherein the one or more quality control parameters include one or more of the shape of the tissue sample, the size of the tissue sample, or one or more mechanical damage.

4. The method of claim 1, further comprising transferring the tissue section to a slide using a transfer medium, wherein the second imaging data comprises imaging data of the tissue section on the transfer medium or imaging data of the tissue section on the slide.

5. The method of claim 4, further comprising comparing at least two of the first imaging data, the imaging data of the tissue section on the transport medium, or the imaging data of the tissue section on the slide.

6. The method described in claim 3, wherein the tissue section is unsuitable if there is no correspondence in shape or size of the tissue sample in the first imaging data and the second imaging data.

7. The method of claim 3, wherein the one or more mechanical damages are selected from the group consisting of tears, shreds, blade marks, wrinkles, cracks, bubbles, insufficient tissue samples, and incomplete tissue samples.

8. The method of claim 7, further comprising identifying a tissue section as unsuitable if one or more mechanical damages are present in the tissue sample in the second imaging data but not present in the tissue sample in the first imaging data.

9. The method of claim 8, further comprising adjusting one or more operating parameters associated with removing the tissue slice to compensate for one or more mechanical damages.

10. The method of claim 8, further comprising approving the tissue section if no mechanical damage is present in the tissue sample in the first imaging data and the second imaging data.

11. The method of claim 8, further comprising rejecting the tissue block if one or more mechanical damages are present in both the first imaging data and the second imaging data.

12. The method of claim 1, wherein one or both of the imaging steps includes illuminating the tissue sample with UV light, imaging the tissue sample with a visible range camera, and creating the first imaging data or the second imaging data.

13. The method of claim 1, further comprising illuminating the tissue section to enhance contrast between the tissue sample and the embedded material within the tissue sample.

14. One or both of the imaging steps comprises: imaging the tissue section in one or more wavelength ranges; generating imaging data of the tissue slice; segmenting the tissue sample from the embedded material based on color and intensity information in the color imaging data; identifying the size, shape, or edge of the tissue sample in the tissue section; The method of claim 1 , comprising:

15. The method of claim 1, further comprising imaging the tissue block prior to removing the one or more sections to generate baseline imaging data for the tissue sample.

16. The method of claim 15, further comprising illuminating the tissue block with UV light.

17. The method of claim 15, further comprising comparing the first imaging data, the second imaging data, or both, with the baseline imaging data.

18. The method of claim 15, further comprising comparing the contour, size, or shape of the tissue sample in the first imaging data, the second imaging data, or both, with the contour, size, or shape of the tissue sample expected from the baseline imaging data.

19. A vision system comprising: an illumination system configured to illuminate the tissue section; an imaging system configured to generate imaging data of the tissue section illuminated by the illumination system; a processor in communication with the imaging system to receive the imaging data and perform one or more quality control analyses based on the imaging data; A vision system comprising:

20. The vision system of claim 19, wherein the one or more quality control analyses are one or more of a comparative analysis of a tissue block and the tissue section on a slide, an analysis of the mechanical properties of the tissue section, an analysis of the sufficiency of the tissue sample, or an analysis of sample representation on a slide.

21. A histology system comprising: a microtome configured to generate one or more tissue sections from the tissue block; a transfer system configured to transfer the one or more tissue sections from the microtome to one or more slides; 1. A vision system comprising: an illumination system configured to illuminate the tissue sample; an imaging system configured to generate imaging data of the tissue section illuminated by the illumination system; a vision system comprising: a processor in communication with the imaging system to receive the imaging data and perform one or more quality control analyses based on the imaging data; A histology system comprising:

22. The histology system of claim 21, wherein the one or more quality control analyses are one or more of a comparative analysis of at least two of the tissue section on the tissue block, the tissue section on the transport system, and the tissue section on a slide, an analysis of the mechanical properties of the tissue section, an analysis of the sufficiency of the tissue sample, or an analysis of sample representation on a slide.

23. A system comprising: an information reader configured to read identification data associated with the tissue block; a microtome configured to cut one or more tissue sections from the tissue block; one or more slides for receiving the one or more tissue sections; a printer configured to receive the identification data and print one or more indicia for the one or more slides after the one or more tissue sections have been cut from the tissue block, the one or more indicia comprising information associating the one or more tissue sections on the one or more slides with the tissue block; and A system comprising:

24. The system described in claim 23, further comprising a transport medium configured to transport the one or more tissue sections from the microtome to the one or more slides.

25. The system described in claim 24, wherein the transport medium includes markings indicating the identification data regarding the one or more tissue sections, the markings being configured to associate the one or more tissue sections with the tissue block.

26. The system described in claim 24, further comprising a transfer medium marking device for marking the transfer medium with markings indicating the identification data relating to the one or more tissue sections, the markings being configured to associate the one or more tissue sections with the tissue block.

27. ​​The system described in claim 23, further comprising a visualization system configured to track the one or more tissue sections from the microtome to the one or more slides.

28. The system described in claim 27, wherein the visualization system is configured to perform a comparison between the one or more tissue sections on the one or more slides and one or more images of the tissue block or images of the sections on a transport medium.

29. The system described in claim 28, wherein the visualization system is configured to make a comparison between the one or more tissue sections on the one or more slides, on the tissue block, or on the transport medium and a baseline image of the tissue sample in the tissue block generated by imaging the tissue block with UV light prior to removing the one or more sections from the tissue block.

30. The system described in claim 29, wherein the comparison is based on the size, shape, and contour of the tissue sample in the one or more tissue sections.

31. The system described in claim 27, wherein the visualization system is configured to read the one or more markers on the slide and verify their association with the identification data for the sample block.

32. The system described in claim 23, wherein the printer prints the label individually for the one or more samples.

33. A system comprising: an information reader configured to read identification data from the tissue block; a microtome configured to cut one or more tissue sections from the tissue block; a transfer medium configured to transfer the one or more tissue sections to one or more slides; A printer and a processor configured to receive the identification data, cause the microtome to cut the one or more tissue sections, and subsequently cause the printer to print one or more indicia for the one or more slides, the one or more indicia comprising information associating the one or more tissue sections on the one or more slides with the tissue block; A system comprising:

34. The system described in claim 33, wherein the transport medium includes markings indicating the identification data regarding the one or more tissue sections, the markings being configured to associate the one or more tissue sections with the tissue block.

35. The system described in claim 33, further comprising a transfer medium marking device for marking the transfer medium with markings indicating the identification data relating to the one or more tissue sections, the markings being configured to associate the one or more tissue sections with the tissue block.

36. The system of claim 33, further comprising a visualization system configured to track the one or more tissue sections from the microtome to the one or more slides.

37. The system described in claim 33, further comprising a visualization system configured to perform a comparison between the one or more tissue sections on the one or more slides and the one or more sections on the tissue block.

38. The system described in claim 37, wherein the comparison is based on the size and edges of the tissue in the one or more tissue sections.

39. A method for tracking a sample in a microtomy, said method comprising: reading identification data from the tissue block; cutting a first set of one or more tissue sections from the tissue block; printing one or more indicia on one or more slides following cutting, the one or more indicia comprising information associating the one or more tissue sections on the one or more slides with the tissue block; transferring said one or more tissue sections to one or more slides and labeling said one or more slides with said one or more labels; A method comprising:

40. The method of claim 39, further comprising comparing the one or more tissue sections on the slide with the one or more tissue sections on the block to confirm an association between the one or more tissue sections on the one or more slides and the tissue block.

41. The method of claim 39, further comprising cutting a second set of one or more tissue sections only after the first set of one or more tissue sections have been placed on the one or more slides and labeled with the one or more labels.

42. The method of claim 39, further comprising comparing the one or more tissue sections on the one or more slides to a baseline image of the tissue sample in the tissue block generated by imaging the tissue block with UV light prior to removing the one or more sections from the tissue block.

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