Preliminary diagnosis of tissue sections

Abstract

A system for optical response measurement of a tissue sample, the system including: a microtome configured to section one or more tissue sections from a tissue block, the one or more tissue sections including one or more tissue samples; an optical response measurement system including: a transfer medium configured to collect the one or more tissue sections and transfer the one or more tissue sections to one or more slides; an illumination system configured to illuminate the one or more tissue sections; and an imaging system configured to perform imaging analysis on the one or more tissue sections illuminated using the illumination system.

Description

Technical Field

[0001] (Related Applications) This application claims the benefit and priority of U.S. Provisional Patent Application No. 63 / 104,907, filed Oct. 23, 2020, and U.S. Application No. 17 / 451,987, filed Oct. 22, 2021, both of which are incorporated herein by reference in their entireties.

[0002] The present disclosure relates to systems and methods for the preliminary diagnosis of abnormalities in tissue samples from tissue sample blocks based on the measurement of optical reactions of intrinsic tissue properties. In some embodiments, such systems and methods can be used in automated histology devices.

Background Art

[0003] The generation of postage-stamp-sized micron-thick tissue sections for microscopic visualization, a conventional microtome method, is a delicate and time-consuming manual task. In the process, the microtome cuts a tissue block composed of tissue samples encapsulated within a support block of an embedding material such as paraffin wax. The microtome holds a blade aligned to cut slices from one face of the tissue block, i.e., the block cutting face. A common type of rotary microtome linearly oscillates a chuck that holds the block with a cutting face along the blade cutting plane. In combination with an incremental advancement of the block cutting face into the cutting plane, the microtome continuously shaves thin tissue sections from the block cutting face. For sections with paraffin wax embedding media, the operator carefully picks up these tissue sections and floats them on warm water. The water gently removes wrinkles and reduces deformation from cutting. Finally, the operator moves the sections from the water onto microscope slides for further processing.

[0004] In a typical pathology workflow, diagnosis is performed after tissue samples cut from a sample block are placed on slides, stained, and subsequently imaged to detect abnormalities, such as cancer cells. Therefore, in the current process, after the cut tissue sections are transferred to slides, they are stained with H&E (hematoxylin and eosin) and evaluated in the pathology laboratory. If a problem with the tissue is detected, such as cancer cells, a new test is ordered. Often, 1-2 days pass between the initial laboratory assessment of the stained tissue and obtaining additional slides in subsequent sectioning. It would be advantageous to speed up this process, allowing the system or user to identify any abnormalities in the tissue earlier in the process. [Overview of the project] [Means for solving the problem]

[0005] This disclosure overcomes the problems and shortcomings of the prior art.

[0006] In some respects, the present disclosure provides a system for measuring the optical response of tissue samples, the system comprising a microtome configured to section one or more tissue sections from a tissue block, the one or more tissue sections comprising one or more tissue samples; a transfer medium configured to collect one or more tissue sections and transfer one or more tissue sections to one or more slides; an illumination system configured to illuminate one or more tissue sections; and an imaging system configured to perform imaging analysis on one or more tissue sections illuminated using the illumination system.

[0007] In some aspects, the Disclosure provides a system in which the illumination system is configured to illuminate one or more tissue sections using structured light. In some aspects, the Disclosure provides a system in which the imaging system is configured to perform imaging analysis using optical microscopic resolution. In some aspects, the Disclosure provides a system in which the imaging system includes a microscope scanning device. In some aspects, the Disclosure provides a system in which the optical reaction measurement system is mounted on a movable stage so that imaging analysis of one or more tissue sections is performed in a microtome on a transport medium or on one or more slides.

[0008] In some respects, the present disclosure provides a system for optical reaction measurement of tissue samples, the system comprising: an optical reaction measurement system comprising: a microtome configured to section one or more tissue sections from a tissue block, the one or more tissue sections comprising one or more tissue samples; an illumination system configured to illuminate one or more tissue sections; an imaging system configured to perform imaging analysis of one or more tissue sections illuminated using the illumination system; and a processor communicating with the optical reaction measurement system, the processor programmed to receive imaging data from the optical reaction measurement system indicating imaging analysis, present the imaging data for analysis of one or more tissue sections, and determine the presence or absence of one or more anomalies.

[0009] In some aspects, the Disclosure provides a system in which a processor is programmed to perform an analysis of imaging data and determine the presence or absence of one or more abnormalities in one or more tissue samples of one or more tissue sections. In some aspects, the Disclosure provides a system further comprising a transport medium configured to collect one or more tissue sections and transport one or more tissue sections to one or more slides. In some aspects, the Disclosure provides a system in which one or more abnormalities include one or more biomarkers indicating a disease, a quality control problem, or a combination thereof. In some aspects, the Disclosure provides a system in which a processor is programmed to perform a diagnostic algorithm and generate a diagnostic value for one or more tissue samples. In some aspects, the Disclosure provides a system in which the diagnostic value indicates the presence or absence of a disease.

[0010] In some aspects, the Disclosure provides a system in which a processor is further programmed to acquire one or more additional tissue sections if the diagnostic value indicates the presence of disease. In some aspects, the Disclosure provides a system in which a processor is configured to identify one or more biomarkers indicating disease in one or more tissue samples from imaging data and to assign diagnostic values ​​for one or more tissue samples based on the one or more biomarkers. In some aspects, the Disclosure provides a system in which a processor is programmed to implement quality control algorithms and identify one or more quality control problems. In some aspects, the Disclosure provides a system in which an illumination system is configured to illuminate one or more tissue sections using structured light. In some aspects, the Disclosure provides a system in which an imaging system is configured to perform imaging analysis using optical microscopy resolution. In some aspects, the Disclosure provides a system in which imaging data includes one or more images of one or more tissue sections. In some respects, this disclosure provides a system in which a processor is configured to present to a human user the imaging data as one or more images of one or more tissue sections.

[0011] In some respects, the present disclosure provides a system for optical reaction measurement of tissue samples, the system comprising: a microtome configured to section one or more tissue sections from a tissue block, the one or more tissue sections comprising one or more tissue samples; a transfer medium configured to collect one or more tissue sections and transfer one or more tissue sections to one or more slides; an illumination system configured to illuminate one or more tissue sections; an imaging system configured to perform imaging analysis on one or more tissue sections illuminated using the illumination system; and a processor configured to receive imaging data indicating imaging analysis from the optical reaction measurement system, perform analysis of one or more tissue samples for one or more biomarkers indicating disease, and, if one or more biomarkers are detected, to cause the microtome to section an additional one or more tissue sections.

[0012] In some respects, the present disclosure provides a method for measuring the optical response of a tissue sample, the method comprising: sectioning one or more tissue sections from a tissue block using a microtome, wherein the one or more tissue sections contain one or more tissue samples; transferring the one or more tissue sections from the microtome to one or more slides using an automated transfer medium; illuminating the one or more tissue sections with an illumination system; and performing imaging analysis with an imaging system to collect imaging data for the one or more tissue sections illuminated by the illumination system.

[0013] In some aspects, the Disclosure provides a method further comprising the step of presenting imaging data to one or more users as one or more images of one or more tissue sections. In some aspects, the Disclosure provides a method further comprising the step of presenting a human user with one or more images of one or more tissue samples after the tissue samples have been stained. In some aspects, the Disclosure provides a method further comprising the step of having a processor receive imaging data indicating an imaging analysis, having the processor analyze the tissue samples, and determining the presence or absence of one or more abnormalities in one or more tissue samples. In some aspects, the Disclosure provides a method further comprising the step of having a processor implement a diagnostic algorithm, generate a diagnostic value for one or more tissue samples indicating the presence or absence of disease in one or more tissue samples, and presenting the diagnostic value to a human user along with one or more images of one or more tissue sections. In some respects, the present disclosure provides a method which further includes the step of having a processor implement a diagnostic algorithm and generate a diagnostic value for one or more tissue samples indicating the presence or absence of a disease. The present invention provides, for example, the following: (Item 1) A system for measuring the optical reaction of tissue samples, wherein the system is A microtome configured to section one or more tissue sections from a tissue block, wherein the one or more tissue sections comprise one or more tissue samples, A transfer medium configured to collect one or more tissue sections and transfer the one or more tissue sections to one or more slides, An optical reaction measurement system comprising: an illumination system configured to illuminate one or more tissue sections; and an imaging system configured to perform imaging analysis on the one or more tissue sections illuminated using the illumination system. A system equipped with these features. (Item 2) The lighting system according to item 1, configured to illuminate one or more tissue sections using structured light. (Item 3) The imaging system described in item 1 is configured to perform the imaging analysis using optical microscopic resolution. (Item 4) The imaging system is a system according to any one of items 1-3, comprising a microscope scanning device. (Item 5) The optical reaction measurement system is the system according to any one of items 1-3, wherein the optical reaction measurement system is mounted on a movable stage so that imaging analysis of the one or more tissue sections is performed in the microtome, on the transport medium, or on the one or more slides. (Item 6) A system for measuring the optical reaction of tissue samples, wherein the system is A microtome configured to section one or more tissue sections from a tissue block, wherein the one or more tissue sections comprise one or more tissue samples, An optical reaction measurement system comprising: an illumination system configured to illuminate one or more tissue sections; and an imaging system configured to perform imaging analysis of the one or more tissue sections illuminated using the illumination system; A processor that communicates with the optical reaction measurement system, wherein the processor receives imaging data from the optical reaction measurement system indicating the imaging analysis, presents the imaging data for the analysis of one or more tissue sections, and is programmed to determine the presence or absence of one or more abnormalities. A system equipped with these features. (Item 7) The system according to item 6, wherein the processor is programmed to perform an analysis of the imaging data and to determine the presence or absence of one or more abnormalities in one or more tissue samples of one or more tissue sections. (Item 8) The system according to item 6, further comprising a transfer medium configured to collect one or more tissue sections and to transfer the one or more tissue sections to one or more slides. (Item 9) A system as described in item 6, comprising one or more biomarkers indicating a disease, a quality control problem, or a combination thereof, including one or more abnormalities. (Item 10) The system according to item 6, wherein the processor is programmed to perform a diagnostic algorithm and generate diagnostic values ​​for one or more tissue samples. (Item 11) The diagnostic value is the system described in item 10, indicating the presence or absence of a disease. (Item 12) The system according to item 11, wherein the processor is further programmed to obtain one or more additional tissue sections if the diagnostic value indicates the presence of the disease. (Item 13) The system according to any one of items 6-12, wherein the processor is configured to identify from the imaging data one or more biomarkers indicating disease in one or more tissue samples, and to assign diagnostic values ​​for one or more tissue samples based on the one or more biomarkers. (Item 14) The system according to any one of items 6-12, wherein the processor is programmed to implement a quality control algorithm and identify one or more quality control problems. (Item 15) The lighting system described in any one of items 6-12 is configured to illuminate one or more tissue sections using structured light. (Item 16) The imaging system is configured to perform the imaging analysis using optical microscopic resolution, as described in any one of items 6-12. (Item 17) The imaging data comprises one or more images of one or more tissue sections, according to any one of items 6-12. (Item 18) The system according to any one of items 6-12, wherein the processor is configured to present the imaging data to a human user as one or more images of one or more tissue sections. (Item 19) A system for measuring the optical reaction of tissue samples, wherein the system is A microtome configured to section one or more tissue sections from a tissue block, wherein the one or more tissue sections comprise one or more tissue samples, A transfer medium configured to collect one or more tissue sections and transfer the one or more tissue sections to one or more slides, An optical reaction measurement system comprising: an illumination system configured to illuminate one or more tissue sections; and an imaging system configured to perform imaging analysis on the one or more tissue sections illuminated using the illumination system; A processor, wherein the processor receives imaging data from the optical reaction measurement system indicating the imaging analysis, performs an analysis of the one or more tissue samples for one or more biomarkers indicating a disease, and, if the one or more biomarkers are detected, is programmed to section an additional one or more tissue sections in the microtome. A system equipped with these features. (Item 20) The system according to item 19, wherein the processor is programmed to perform an analysis of the imaging data and to determine the presence or absence of one or more abnormalities in one or more tissue sections or tissue samples. (Item 21) A system as described in item 19, comprising one or more biomarkers indicating a disease, a quality control problem, or a combination thereof, including one or more abnormalities. (Item 22) The system according to item 19, wherein the processor is programmed to perform a diagnostic algorithm and generate diagnostic values ​​for one or more tissue samples. (Item 23) The diagnostic value is the system described in item 22, indicating the presence or absence of a disease. (Item 24) The system according to item 23, wherein the processor is further programmed to obtain one or more additional tissue sections if the diagnostic value indicates the presence of the disease. (Item 25) The system according to any one of items 19-24, wherein the processor is configured to identify from the imaging data one or more biomarkers indicating disease in one or more tissue samples, and to assign diagnostic values ​​for one or more tissue samples based on the one or more biomarkers. (Item 26) The system according to any one of items 19-24, wherein the processor is programmed to implement a quality control algorithm and identify one or more quality control problems. (Item 27) The lighting system described in any one of items 19-24 is configured to illuminate one or more tissue sections using structured light. (Item 28) The imaging system is configured to perform the imaging analysis using optical microscopic resolution, as described in any one of items 19-24. (Item 29) The imaging data comprises one or more images of one or more tissue sections, according to any one of items 19-24. (Item 30) The system according to any one of items 19-24, wherein the processor is configured to present the imaging data to a human user as one or more images of one or more tissue sections. (Item 31) A method for measuring the optical reaction of a tissue sample, wherein the method is Sectioning one or more tissue sections from a tissue block using a microtome, wherein each one or more tissue section comprises one or more tissue samples. Transferring one or more tissue sections from the microtome to one or more slides using an automated transfer medium, The lighting system illuminates one or more of the aforementioned tissue sections, The imaging system performs imaging analysis and collects imaging data for one or more tissue sections illuminated by the illumination system. Methods that include... (Item 32) The method according to item 31, further comprising presenting the imaging data to one or more users as one or more images of the one or more tissue sections. (Item 33) The method according to item 31, further comprising presenting a human user with an image of one or more of the one or more of the tissue samples after the tissue samples have been stained. (Item 34) The method according to any one of items 31-33, further comprising: a processor receiving imaging data indicating the imaging analysis; the processor analyzing the tissue samples and determining the presence or absence of one or more abnormalities in the one or more tissue samples. (Item 35) The method according to item 34, further comprising using the processor to perform a diagnostic algorithm, generate a diagnostic value relating to the one or more tissue samples indicating the presence or absence of disease in the one or more tissue samples, and presenting the diagnostic value to a human user along with an image of one or more of the one or more tissue sections. (Item 36) The method according to item 34, further comprising using the processor to perform a diagnostic algorithm and generate a diagnostic value for one or more tissue samples indicating the presence or absence of disease. [Brief explanation of the drawing]

[0014] This disclosure is further described in the following detailed description with reference to several drawings, which are described as non-limiting embodiments of exemplary embodiments, where similar reference numbers represent similar parts throughout several of the drawings.

[0015] [Figure 1] Figures 1, 2, and 3 illustrate embodiments of the illumination and imaging systems of this disclosure. [Figure 2] Figures 1, 2, and 3 illustrate embodiments of the illumination and imaging systems of this disclosure. [Figure 3] Figures 1, 2, and 3 illustrate embodiments of the illumination and imaging systems of this disclosure.

[0016] [Figure 4] Figure 4-6 provides a flowchart illustrating various non-limiting embodiments of the method according to this disclosure. [Figure 5] Figure 4-6 provides a flowchart illustrating various non-limiting embodiments of the method according to this disclosure. [Figure 6] Figure 4-6 provides a flowchart illustrating various non-limiting embodiments of the method according to this disclosure.

[0017] [Figure 7A] Figure 7A illustrates an exemplary automated microtome according to this disclosure.

[0018] [Figure 7B] Figure 7B is a schematic diagram of one embodiment of the automated tape transfer device of the present disclosure.

[0019] [Figure 8] Figure 8 is a schematic diagram showing the tape prior to being applied to the surface of a sample block.

[0020] [Figure 9] Figure 9 is a perspective view of the slide station and optical reaction measurement system of the automated apparatus shown in Figure 6.

[0021] [Figure 10] Figure 10-12 provides flowcharts illustrating various non-limiting embodiments of the automation method according to this disclosure. [Figure 11] Figure 10-12 provides flowcharts illustrating various non-limiting embodiments of the automation method according to this disclosure. [Figure 12] Figure 10-12 provides flowcharts illustrating various non-limiting embodiments of the automation method according to this disclosure.

[0022] [Figure 13] Figure 13 is a schematic illustration of a high-level architecture for implementing the process, as described in this disclosure.

[0023] [Figure 14] Figure 14 is a flowchart illustrating an exemplary method of the present disclosure.

[0024] [Figure 15] Figure 15 illustrates an image of an illuminated tissue section from the aspect of this disclosure.

[0025] The drawings identified above illustrate embodiments of the disclosed embodiments, but other embodiments are also conceivable, as described in the discussion. This disclosure presents illustrative embodiments, not as an limitation, but as an expression. Numerous other modifications and embodiments falling within the scope and spirit of the principles of the disclosed embodiments can be devised by those skilled in the art. [Modes for carrying out the invention]

[0026] Detailed explanation This disclosure provides a system and method for measuring the optical reaction of tissue samples without chemical staining or labeling of the tissue during the preparation of the tissue samples in a histological process. The methods and systems disclosed herein can be used in either a manual, semi-automated, or fully automated histological process to perform imaging analysis of unstained tissue samples. Imaging analysis is performed, for example, using an imaging system to obtain imaging data showing an image of one or more illuminated tissue sections. The imaging data may be an actual image of the tissue sample or data showing an image, for example, data that can be used to reconstruct an image of the tissue sample, and the terms can be used synonymously. Based on the imaging data, decisions about further progress of the tissue sample can be made either by a human user or by a computer system. Such decisions can be made based solely on the imaging data or in combination with other information about the tissue sample.

[0027] In some embodiments, the systems and methods of the Disclosure may provide images of one or more tissue samples that can be used to diagnose a disease or condition. Note that the term “diagnosis” as used herein refers to a singular, e.g., a single disease, but also encompasses more than one, e.g., multiple diseases, as in the term “diagnoses.” In some embodiments, the reaction measurement systems and methods of the Disclosure enable information relevant to a diagnosis, e.g., the presence of a tumor, to be extracted from the tissue during a slide preparation process, e.g., tissue sectioning. In some embodiments, the systems disclosed may be used to determine whether a tissue section suffers from one or more quality issues (e.g., insufficient tissue sample, not an intact tissue sample). The systems and methods make a preliminary diagnosis using inherent tissue properties without any staining or special treatment, such as labeling the tissue with a fluorescent signal. This provides a preliminary, rapid set of information during tissue sample preparation, which helps prioritize tissue samples for processing, thereby accelerating diagnostic time for cases where abnormalities are already visible in unstained images. Information from unstained / unprocessed tissue images can be integrated with information from downstream stained sections, which can accelerate computer-aided diagnosis. Thus, optical imaging methods for computer-aided diagnosis can be integrated into automated equipment. Multiple internal levels of tissue response measurements can be provided due to different stages in the process in some embodiments, e.g., analysis of tissue in new slices from blocks, slices on transport, and slices on slides.

[0028] In some embodiments, the diagnosis can be performed by a human user. The methods and systems of this disclosure can accelerate the process of tissue sample preparation, which involves multiple steps of tissue sectioning, staining, and analysis. The methods and systems can provide images to a human user (e.g., a pathologist) while the sections are still in an early stage of processing, so that the human user can request, for example, additional tests (staining or molecular tests). This can accelerate the diagnostic process, which improves healthy outcomes for patients.

[0029] This disclosure provides systems and processes for preliminary diagnosis of tissue sections from tissue sample blocks by a computer system, a human user, or both, without chemical staining or alternative labeling of the tissue. In some embodiments, the methods and systems of this disclosure utilize optical methods during histological slide preparation, e.g., on the block plane, during tape transfer, or on the slide, to acquire and interpret imaging data of unstained tissue to assist in diagnosis. This may be referred to as optical staining and can be used at an earlier stage of the slide preparation process, e.g., during sample sectioning or slide preparation, to extract diagnostic information. However, in some embodiments, the methods and systems rely on intrinsic tissue properties (e.g., endogenous phosphors present in the tissue) without any staining or special treatment. Intrinsic tissue properties are used without any staining or special treatment and therefore accelerate the process. In other words, sections of natural unstained tissue can be analyzed using various optical reaction measurement techniques. Thus, a preliminary, rapid set of information from automated devices is provided during the sectioning process, which helps prioritize samples for processing and thus speeds up diagnostic time for cases where abnormalities are already visible in unstained images. In addition, integrating unstained section information with downstream stained section information can speed up the final computer-aided diagnosis (CAD). In some embodiments, the preliminary diagnostic system / process is integrated into an automated tissue transfer system that utilizes tape (or other transfer medium) to transport tissue sections cut by a microtome from a tissue sample block to a microscope slide.

[0030] In some embodiments, the Disclosure provides an optical reaction measurement system comprising an illumination system and an imaging system. The illumination system can illuminate tissue at various wavelengths. The imaging system can image the illuminated tissue at various wavelengths by utilizing a wide range of optical phenomena, including, but not limited to, selective absorption, fluorescence of different endogenous phosphors in the tissue, the Raman effect, and similar phenomena. The imaging system can also provide imaging of the tissue section across its area, for example, scanning the entire tissue section.

[0031] In some embodiments, the systems and methods of the Disclosure are configured to provide images of tissue sections so that an assessment can be made for the presence or absence of cancer cells or other abnormalities, e.g., the presence or absence of disease biomarkers or quality issues. In some embodiments, after such an assessment, feedback can be provided to a pathology laboratory, and in other embodiments, after such an assessment, further sections can be taken for further analysis (e.g., if cancer cells are detected), or no further sections can be taken (e.g., if no abnormalities are detected). In some embodiments, the systems and methods of the Disclosure can be used for preliminary diagnosis of abnormal or disease conditions in gastroenterology, gynecological pathology, hematological disorders, coagulation disorders, microbiology, lung cancer, and breast cancer. In some embodiments, the systems and methods of the Disclosure can be used for preliminary diagnosis of infectious disease pathology. In some embodiments, the methods of the Disclosure can be used to determine whether a tissue sample conforms to quality control parameters such as size, shape, and whether the tissue sample is intact. In some embodiments, the images can be used for non-clinical use, e.g., for preclinical toxicology studies or for animal or agricultural analysis in which histology is used.

[0032] In some embodiments, information is acquired (collected) via imaging using a set of wavelengths, and digital analysis of the results is performed to make a diagnostic decision. Tissue sections can be “optically stained” instead of “chemically stained,” that is, the method and system utilize imaging techniques to analyze intrinsic tissue properties (e.g., endogenous phosphors present in the tissue) without any staining or special treatment of the tissue sample. Such untreated tissue samples can be analyzed at one or more illumination wavelengths using optical imaging techniques, including, for example, fluorescence spectroscopy, Raman, or IR spectroscopy.

[0033] An exemplary process for preparing tissue samples for analysis is described in context. Tissue samples are provided as tissue blocks or sample blocks, with the tissue embedded in a preservation material such as paraffin. New blocks first undergo sectioning, which involves removing a 0.1-1 mm layer of paraffin wax on the tissue sample, exposing the tissue beneath. This process of removing the paraffin layer and exposing larger sections of the tissue is called "block sectioning." The tissue block can then be hydrated, returned to a microtome, and sectioned. Sections of the tissue sample are transferred to glass slides for analysis and mounted thereon.

[0034] The systems and methods of this disclosure can be used for preliminary diagnosis, imaging, or other information gathering techniques of tissue samples during the slide preparation process, based on the inherent properties of the tissue sample, without any staining or other special treatment. Typically, for histological analysis, the tissue sample on the slide is stained with H&E dyes (hematoxylin and eosin) or other (special) dyes, etc., to provide the pathologist with a detailed view of the tissue. By staining the cellular structure, otherwise transparent tissue sections are colored, enabling disease diagnosis based on the cellular organization and the abnormalities shown. The systems and methods of this disclosure utilize one or more optical or imaging techniques (optical staining) to provide preliminary diagnosis of untreated tissue samples.

[0035] Referring to Figure 1, in some embodiments of the present disclosure, the optical reaction measurement system 10 may comprise an illumination system 1 and an imaging system 2. The illumination system 1 illuminates a tissue sample 4 (shown in a microtome chuck 3) to assist in tissue analysis using the imaging system 2. The illumination system 1 may also be used to illuminate the tissue sample in a tissue section, and the imaging system 2 is used to perform imaging analysis of the tissue sample. Based on this analysis, imaging data for the tissue section may be used for diagnostic, quality control, or other decision-making purposes. In some embodiments, the optical reaction measurement system 10 may acquire imaging data from a plurality of consecutive tissue sections, and such imaging data may be used for three-dimensional reconstruction of the tissue sample or for comparison.

[0036] In some embodiments, tissue blocks may be illuminated with structured light, and the reflected light can be used for tissue diagnosis. In some embodiments, structured light refers to illumination of tissue blocks in a specific pattern. In some embodiments, structured light may be spatially structured, i.e., the tissue is illuminated in a geometrically structured pattern such as a grid, stripes, or concentric circles. In some embodiments, structured light may be spectrally structured, i.e., the tissue is illuminated simultaneously with light having different wavelengths. In some embodiments, the wavelengths may be selected from different intensities, bands, or colors. In some embodiments, spectrally structured light may be within the same or primarily the same intensity range (e.g., UV), but may have different specific wavelengths within that intensity range. In some embodiments, spectrally structured light may consist of light from one or more frequency bands, such bands tuned to the optical properties of tissue molecules, such optical properties including, for example, fluorescence absorption and emission spectra. As an example, a wavelength range with primarily UV emission may produce strong autofluorescence from a certain tissue compartment, facilitating subsequent diagnostic steps. In some embodiments, the structured light may be sequentially structured, for example, tissue samples may be illuminated sequentially at various times with the same or different time intervals between illuminations.

[0037] Illumination system 1 can be configured to illuminate a tissue sample at one or more wavelengths across a certain range of wavelengths. Different scanning or diagnostic applications can use different ranges. For example, one or more wavelengths within the 380 nm to 450 nm range can cause certain proteins in the tissue to fluoresce. Another range of the spectrum, within the 620 nm to 4,000 nm range, can be absorbed by certain proteins. Illumination system 1 can illuminate a tissue sample, and therefore it can be imaged under different contrast conditions. In some embodiments, certain proteins may be illuminated to fluoresce, which can create contrast, for example, between the tissue sample and the implantation material, or between parts of the tissue sample. In some embodiments, absorption spectra can be used to create dark spots in the tissue sample, and IR wavelengths can be used to create contrast and detect certain proteins. In some embodiments, images collected under different illumination conditions that create different contrast maps can be combined to provide richer information to a diagnostic algorithm or user. For example, reference numeral 6 illustrates a block under high-contrast illumination where the contrast between paraffin and tissue is prominent according to the present disclosure, while reference numeral 5 illustrates a sample block under low-contrast illumination where it is more difficult to distinguish between tissue and paraffin.

[0038] The illumination system may include one or more light sources that generate light in the ultraviolet range, visible range, mid-infrared range, or infrared range. For example, UV light can be used to excite natural phosphors in tissues such as NADH (e.g., 325 nm to 375 nm) or FAD (e.g., 425 nm to 475 nm). Suitable light sources include, but are not limited to, LEDs, lasers, supercontinuum light sources, and similars. In some embodiments, the wavelength of light can be controlled using filters or LEDs with wavelength emission within a given range. In some embodiments, on the image acquisition side, filters may be provided to enhance image acquisition.

[0039] The imaging system 2 may include a photodetector and may be configured to image tissue samples for evaluation using one or more imaging methods. The imaging system may be configured for use with various imaging techniques such as fluorescence spectroscopy, Raman spectroscopy, IR spectroscopy, or a combination thereof. Various image processing techniques, such as those described below, may be used for evaluation. Recent artificial intelligence-based image processing techniques may also be used. For example, the optical reaction measurement system 2 may include a visible light detector, such as a camera capable of capturing a digital image of a tissue sample. In some embodiments, the imaging system 2 may include a charge-coupled detector, a thermal detector, a photodetector, or a spectrometer, such as one or more of a spectral, multispectral, or hyperspectral camera. The imaging system 2 may image illuminated tissue sections for spectroscopic analysis, including, but not limited to, fluorescence spectroscopy, Raman spectroscopy, IR spectroscopy, or a combination thereof.

[0040] In some embodiments, the imaging system may be configured to capture an image of the entire tissue sample using micron resolution. In some embodiments, the imaging system may include an optical microscope. In some embodiments, the imaging system may include a hall slide imaging scanner, which may be mounted on a movable stage, to acquire microscopic images of one or more tissue sections.

[0041] The transmission mode of reflection can be utilized. Tissue samples can be illuminated or examined from various angles, such as an angle perpendicular to the front, an angle at the angle of sight, an angle perpendicular to the side, or an angle at the angle of sight, or any combination thereof.

[0042] In some embodiments, the imaging system 2 may include a silicon-based multi-channel array detector, a CCD (charge-coupled device), which can be used as a detector in Raman spectroscopy. During operation, a laser beam illuminates the sample. Electromagnetic radiation from the illuminated spot is collected using a lens and filtered through a monochromator. Elastic scattering radiation (Rayleigh scattering) at wavelengths corresponding to the laser line is filtered out by either a notch filter, an edge-pulse filter, or a bandpass filter, while the remaining collected light is dispersed on the CCD detector, providing a spectral distribution of the electromagnetic radiation collected from the sample. This spectral distribution corresponds to the spectral signature composition of a substance in the sample's composition. Analysis of the spectral distribution leads to the identification of a substance in the sample.

[0043] The images can be processed and evaluated in relation to binary determination of anomalies, e.g., the presence or absence of cancer cells. As mentioned above, such analysis relies on the inherent properties of the tissue without any additional chemical processing. For example, in relation to cancer diagnosis, an illumination system is used to illuminate the tissue sample using UV light (e.g., one or more wavelengths within the range of 275 nm to 285 nm), and the reflected light can be detected using an imaging system 2 (e.g., a CCD camera). The spectral distribution between healthy and malignant tissues differs, and differences exist, e.g., in spatial cell distribution patterns, the concentration of certain proteins, and molecules. The collected data may be used by algorithms to make decisions regarding the diagnosis, or provided to human experts to make those decisions.

[0044] It should be understood that the various illumination and imaging subsystems and various associated methodologies described herein are provided as examples, as other illumination systems may be used to enhance the distinction between tissue and paraffin (or other implanting material), other imaging systems may be used, and other calculation systems may be used for preliminary diagnosis without (or prior to) staining or labeling the tissue. Furthermore, any combination of illumination systems and / or imaging systems may be used.

[0045] Light (coherent or non-coherent) can be used through absorption, refraction, scattering, Raman scattering, fluorescence, phosphorescence, and interference, and wavelength can be a continuous or discontinuous distribution at any point in the spectrum from X-rays to radio waves, or any combination of these modalities.

[0046] In some embodiments, the methods and systems disclosed herein can be used in connection with manual processes for tissue preparation. In some embodiments, the systems and methods disclosed herein can be incorporated into an automated histology apparatus as part of an automated system for preparing tissue samples. The automated methods (processes) and systems disclosed herein can automatically section a tissue block via a fully automated sectioning device, and once sectioned, the tissue is automatically cut from the block plane and automatically transferred to a tape, which is automatically moved via rollers to advance the cut tissue and position the trailing portion of the tape across the block plane for subsequent transfer of the cut tissue section to the tape. In some embodiments, the automated tissue sectioning apparatus also includes a slide station, and the tissue sections held on the tape are automatically transported and transferred to glass slides for analysis within the automated apparatus. In some embodiments, a transfer mechanism such as tape transfer can be used to transfer tissue sections from a microtome to a glass slide. Note that transfer media other than tape (also referred to as transport media) may also be available. Therefore, since the systems and methods disclosed herein are fully applicable not only to tape but also to other transfer media, references to tape herein are used for convenience only.

[0047] The optical reaction measurement system 10 can be positioned to visualize tissue samples at different steps in the sample preparation process. In some embodiments, as shown in Figure 1, the optical reaction measurement system may be positioned to illuminate and visualize a sample block 4 when the sample block is supported on a sample support chuck 3. Referring to Figure 2, in some embodiments, the optical reaction measurement system is positioned to diagnose a cut tissue sample while it is being transported by a transport medium 12, which is driven by an electric feeding mechanism 13. Referring to Figure 3, alternatively or in addition, the optical reaction measurement system 10 can be positioned to diagnose a tissue section on a slide at a slide station 7. After it has been cut from the block and attached to tape, an image of the cut tissue section on the tape (or other transport medium) can be taken. In addition or alternatively, after it has been transported to a slide, an image of the cut tissue section can be taken. The pathology system of this disclosure may include multiple optical reaction measurement systems at various locations, or it may include a single optical reaction measurement system that can be moved between different locations.

[0048] Referring to Figure 4, an exemplary process flowchart 400 for early diagnosis of a sectioned tissue sample is provided. As shown in Figure 4, in some embodiments, in step 401, a microtome cuts a tissue section from a sample block. In step 402, after the microtome has cut the tissue section from the sample block, the tissue section is illuminated and the sectioned section is imaged by an imaging system. In some embodiments, the imaging data may be taken on the tissue sample on the sample block. In step 404, the imaging data is analyzed (by a computer or human user) to detect abnormalities in the tissue. In step 406, if no abnormalities are detected, more tissue sections may not be obtained at that point. In step 408, if abnormalities are detected, more tissue sections are taken from the sample block. In step 410, the sectioned tissue sections from either step 406 or step 408 are transferred to slides for staining and analysis. The microtome may continue to cut and analyze additional sections for any abnormalities. If an abnormality is detected in a subsequent section, an additional section will be acquired. As described above, in some embodiments, the device can perform preliminary diagnosis / analysis and provide feedback regarding human activation of the microtome to acquire more sections. In alternative embodiments, instead of or in addition to the machine, a pathologist performs preliminary diagnosis / analysis during the sectioning / imaging process and controls the activation of the microtome regarding additional sections.

[0049] In the process depicted in flowchart 500 of Figure 5, in some embodiments, in step 501, after the microtome cuts tissue sections from the sample block, in step 502, the tissue sections are illuminated and imaging data of the cut sections are acquired by the imaging system, either at the time of transfer or immediately after transfer to tape. In step 504, the imaging data is analyzed to detect abnormalities in the tissue. In step 506, if no abnormalities are detected, more tissue sections may not be obtained at that point. In step 508, if abnormalities are detected, more tissue sections are taken from the sample block. In step 510, the cut tissue sections from either step 506 or step 508 are transferred to slides for staining and analysis. Thus, a preliminary diagnosis for binary determination of the presence or absence of abnormalities and the need for additional sections is performed on tape by machine and / or pathologist.

[0050] In the system / method described in flowchart 600 of Figure 6, the system / method may be identical to that in Figure 5, except that images of the cut sections are taken on slides instead of on tape. In step 601, in some embodiments, a microtome cuts tissue sections from a sample block. In step 62, the tissue sections are illuminated, and imaging data of the cut sections are acquired by the imaging system, either at the time of transfer or immediately after transfer to tape. In step 604, the imaging data is analyzed to detect abnormalities in the tissue. In step 606, if no abnormalities are detected, more tissue sections may not be taken at that point. In step 608, if abnormalities are detected, more tissue sections are taken from the sample block. In step 610, the cut tissue sections from either step 606 or step 608 are transferred to slides for staining and analysis. Thus, a preliminary diagnosis for binary determination of the presence or absence of abnormalities and the need for additional sections is performed on the slides by machine and / or pathologist. As mentioned above, photographs of tissue samples may be taken in one or more locations on blocks, tapes, and slides, and in addition to or instead of one or more photographs being taken on blocks, tapes, or slides, one or more photographs may also be taken in one or more locations (e.g., on slides).

[0051] Referring to Figure 7A, the optical reaction measurement system of this disclosure may be part of an automated microtome device. In some embodiments, the automated microtome device 100 may include a combination of mechanisms for receiving a sample block, cutting a sample / section from the sample block, and transferring the cut sample onto a tape to be transferred to a slide for analysis. The combination of mechanisms may include at least one microtome 104, a transfer medium 106, a slide adhesive coater 112, a slide printer 114, a slide input rack 116, a slide singulator 118 for selecting a slide from a stack of slides, and a slide output rack 120. This combination of mechanisms works together to prepare the sample on the slide and to prepare the slide itself.

[0052] At least one microtome 104 is configured to cut tissue samples or sections from a tissue block, which is enclosed within a support block of preservation material such as paraffin wax. After sectioning, the tissue sections can then be transferred onto a transfer medium 106 such as tape for subsequent transfer to a slide station for pathology or histology.

[0053] As described above, the optical reaction measurement system of this disclosure can be installed in one or more locations within the automated microtome device 100. Figure 7B is a schematic diagram of one embodiment of an automated tape transfer device (system) illustrating the apparatus, in which an illumination and imaging (vision) system and a preliminary diagnostic system may be used. The path of the transfer medium 12 for transporting the cut tissue sections after the block has been fully sectioned is illustrated. Figure 7B shows a microtome 14 used to hold the sample block and cut the sections. The microtome 14 includes a blade (not shown) aligned to cut slices (or sections) from the face of the tissue block.

[0054] In addition to the adhesive transfer medium 12 and the microtome 14, the automated tape transfer device of Figure 7B includes an electric feeding mechanism 13, a tape applicator 17, a slide station 15, and a winding mechanism 16. An illumination system 1 and an imaging system 2 for the transfer medium 12 (e.g., adhesive tape) are shown (diametrically) in the drawings. The same (1, 2) or different illumination and imaging systems may be used for the sample block. An illumination system 1a and an imaging system 2a for the slide are also shown (diametrically) in the drawings. However, as described above, alternatively or in addition, the system of the present disclosure may include only one optical reaction measurement system that can be moved between different locations.

[0055] The transport medium 12's path begins at the feeding mechanism 13 and proceeds toward the microtome 14 and the applicator end of the tape applicator 17. The transport medium is then applied to the surface of the tissue block, which, after sectioning from the tissue block, picks up the tissue section. The transport medium 12 then moves away from the microtome and toward the slide station 15, and finally is stored on the winding mechanism 16. A controller-controlled motorized reel moves the portion of the adhesive tape containing the cut section away from the microtome and sample block, and advances the adhesive tape so that a new portion of the adhesive tape is positioned on the cut surface and adhered for the next section to be cut by the microtome and transferred to the adhesive tape.

[0056] As the cycle begins, the tape applicator 17 moves toward the cut surface 22 of the tissue sample block 24 (Figure 8). This causes the roller member 25 of the tape applicator 17 to press the transfer medium 12, for example, if adhesive tape is used, the adhesive side of the tape, onto the cut surface 22, causing the transfer medium 12 to adhere and cover the entire cut surface 22 with the transfer medium 12. The tape applicator 17 then retracts in the opposite direction, resetting the roller member 25 to its original position away from the cut surface 22. In an alternative embodiment, the cut tissue section is moved to come into contact with the tape after sectioning by microtome.

[0057] Figure 9 shows a slide station 15 of the automated tape transfer device in more detail. The slide station 15 may be a UV station for transferring tissue sections on the transfer medium 12 to a microscope slide 40 that is pre-coated with a UV-curable adhesive. Rollers may then press the sections on the adhesive tape onto the slide. While the system in Figure 6 includes a slide station for transfer to the slide, it should be understood that in some embodiments of this system, the system does not include a slide station, and after the transfer of the cut sections to the tape and the transfer of the tape from the microtome area, the sections may be transferred from the tape to the slide by other means, such as manual transfer or storage on the tape.

[0058] The slide station 7 comprises a lower portion 30 with spacers 32 that create a slide slot, a support section 34, a UV source 36, and a motor 38. The slide slot created by the spacers 32 and the support section 34 hold the slide 40. The motor 38 is used to move or translate the lower portion 30 of the slide station 15 to adjust the position of the section on the slide 40 so that the exact location where the sample section from the tape is deposited on the slide 40 can be controlled. An illumination and imaging system may be provided in or adjacent to the slide station to illuminate the tissue section on the slide and to take an image of it.

[0059] As described above, the illumination and imaging systems disclosed herein can be used in conjunction with other automated devices, tapes other than adhesive tapes, and devices that do not have automated slide stations, as well as in manual systems.

[0060] The automated system provides the use of a transfer medium, such as adhesive tape, or alternatively, another transfer medium, to support samples from tissue block cuts. The automated system and method also provide automated subsequent transfer of samples from adhesive tape to slides.

[0061] This system is described in conjunction with the use of a continuous strip of adhesive tape, but it should be understood that other transfer media may also be used. The adhesive tape, as disclosed herein, adheres to the cut surface of the sample block prior to sectioning. Following the adhesion of the adhesive tape to the cut surface, the microtome begins the cutting action. The adhesion of the adhesive tape to the cut surface supports the section being cut by the microtome. Once the microtome has completed cutting, the cut section remains adhered to the adhesive tape. In alternative embodiments, the section may be cut first, followed by adhesion to the transfer medium.

[0062] 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 include dry adhesive tapes such as Setex-dA produced by nanoGriptech, which provide a bond via van der Waals forces (molecular bonds) and whose tape peel force varies considerably depending on the peel angle, thereby minimizing section damage during peeling. The tape preferably leaves no residue, adheres when needed, and peels off without damaging tissue when needed. 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 is preferably large enough to completely cover the cut surface of the sample block, i.e., to hold a complete section when it is sliced ​​from the sample block.

[0063] It should be noted that the tape provides one embodiment of a transport device / system for tissue slicing. Other transport systems, such as robotic arms and a series of cups containing water, can also be used. The systems described herein, such as lighting systems and imaging systems, are fully applicable to slices on various transport systems.

[0064] The slides in the slide station can be held stably (firmly) according to some embodiments of the system described herein.

[0065] An automated tape transfer device may include a programmable digital controller, processor, or other type of application-specific integrated circuit (ASIC) used to control the motion of the automated tape transfer device, communicate with the user of the automated tape transfer device, and / or communicate with the microtome to which the automated tape transfer device is connected. Many motions can be controlled within the automated tape transfer device. Examples of these motions include the movement of the feeding and winding mechanisms, the movement of the lower and translational portions of the slide station, and the movement of linear actuator members. The controller may also provide the user with information about the function or condition of the automated tape transfer device, such as the number of slides prepared, the number of sections transferred, and the amount of tape remaining on the roll. The controller may be capable of receiving any type of input (e.g., mechanical, visual, electrical, etc.) to perform its control functions.

[0066] In some embodiments, the automated tape transfer device further includes an optical device for inspecting sample blocks. For example, a microtome may store multiple sample blocks for sectioning. The optical device may be used to assess the conditions of the section or to determine the location of tissue within the embedding medium. In one embodiment, a macro image of the section may allow for more precise placement of adhesive tape on the section. Analysis of the section may facilitate automated trimming of the section to expose the desired tissue for sectioning.

[0067] It should be noted that the use herein of the terms tissue section or section is based on the assumption that initial sections cut from a sample block may not contain much tissue because they may contain the material on which they are placed, such as paraffin or other embedding medium. However, what is important for histopathology is the tissue section, i.e., the tape area containing sufficient tissue sections.

[0068] Referring to the flowchart in Figure 10, after the tape, for example, a tape cartridge, is loaded onto the feeding mechanism, in some embodiments, in step 1001, the feeding mechanism is activated to advance the tape, i.e., a continuous length of adhesive tape. In step 1002, a linear actuator member moves toward the cut surface of the sample block. In step 1004, a roller member presses the adhesive side of the tape onto the cut surface. In step 1006, the roller member is pressed down to adhere the adhesive tape so as to cover the entire cut surface. In step 1008, the linear actuator retracts to reposition the roller member for subsequent application of adhesive. In step 1010, the microtome cuts the section to be covered with adhesive tape. In step 1012, the cut section advances to the slide station to align with the slide. In step 1014, the slide roller presses the covered section onto the slide. In step 1016, the tissue sections are stacked on the slide. In step 1018, the slide roller retracts to its original position. In step 1020, the tape moves forward so as to move away from the slide and is stored on the winding mechanism.

[0069] It should be noted that a single imaging system, such as a digital camera, may be used to acquire imaging data adjacent to the transfer of the cut sections to the adhesive of the tape. The same camera may be repositioned adjacent to the slide station during automated operation to take a photograph of the slide after the transfer of the sections to the slide. Alternatively, a different reaction measurement system may be provided in or adjacent to the slide station to take a photograph after the transfer of the sections to the slide. As described above, the imaging system may acquire imaging data of the cut sections after the transfer of the cut sections to the tape and after the transfer of the cut sections from the tape to the slide, or alternatively, photographs may be taken only after the transfer to the tape or only after the transfer to the slide. Such imaging data may be taken at the time of transfer, immediately after the transfer, or downstream of the transfer (after the tape has advanced past the tape applicator or advanced to the slide station). Photographs of the tape and / or the cut sections of the tape may also be taken at other points during the tape feeding cycle, if desired.

[0070] Referring to Figure 11, an exemplary process flowchart 1100 for detecting anomalies in a cut tissue sample is provided with reference to the flowchart in Figure 11, and after a tape, e.g., a tape cartridge, is loaded onto the feeding mechanism, in some embodiments, in step 1101, the feeding mechanism 13 is activated to advance the tape, i.e., a continuous length of adhesive tape. In step 1102, the tape applicator 17 is moved toward the cut surface of the sample block. Next, in step 1104, a roller member presses the adhesive side of the tape onto the cut surface. In step 1106, the roller member is then pressed down to adhere the adhesive tape so as to cover the entire cut surface. In step 1108, the tape applicator 17 is retracted to its original position to reset the roller for subsequent application of adhesive tape to another sample. In step 1110, a microtome then cuts the section to be covered by the adhesive tape (along a plane parallel or substantially parallel to the cut surface). In step 1112, each section can be illuminated and imaged by an illumination system and an optical reaction measurement system. In step 1114, the imaging data is analyzed to detect abnormalities in the tissue. In step 1116, if no abnormalities are detected, no further tissue sections are requested at that time. In step 1118, if abnormalities are detected, more tissue sections are taken from the sample block, and in step 1120, the cut tissue sections are transferred to slides for staining and analysis. The device will continue to cut and analyze additional sections for abnormalities. If abnormalities are detected in subsequent sections, additional sections will be taken. As described above, in some embodiments, the device can perform preliminary diagnosis / analysis and automatically initiate additional sections for transfer to slides, or alternatively, provide feedback regarding human activation of the device to obtain more sections. In alternative embodiments, instead of or in addition to the machine, a pathologist performs preliminary diagnosis / analysis during the sectioning / imaging process and controls the activation of the device regarding additional sections.

[0071] In the system / method depicted in flowchart 1200 of Figure 12, the system / method is identical to that in Figure 11, except that imaging data of the section is acquired on a slide instead of on tape. In some embodiments, in step 1201, the feeding mechanism is activated to advance the tape. In step 1202, a linear actuator member is moved toward the cut surface of the sample block. Next, in step 1204, a roller member presses the adhesive side of the tape onto the cut surface. In step 1206, the roller member is then pressed down to adhere the adhesive tape so as to cover the entire cut surface. In step 1208, the linear actuator is retracted to its original position to reset the roller for subsequent application of adhesive tape to another sample. In step 1210, the microtome then cuts the section to be covered by the adhesive tape (along a plane parallel or substantially parallel to the cut surface). In step 1212, the section is advanced to the slide station to align with the slide. In step 1214, each section can be illuminated and imaged by an illumination system and an optical reaction measurement system. In step 1216, the imaging data is analyzed to detect abnormalities in the tissue. In step 1218, if no abnormalities are detected, no further tissue sections are requested at that time. In step 1220, if abnormalities are detected, more tissue sections are taken from the sample block, and in step 1222, the cut tissue sections are transferred to slides for staining and analysis. Thus, a preliminary diagnosis for binary determination of the presence or absence of abnormalities and the need for additional sections is performed on the slides by a machine and / or pathologist, as illustrated in conjunction with the chart in Figure 11.

[0072] The analysis of imaging data using the flowcharts in Figures 11 and 12 can be enhanced by the use of illumination and optical reaction measurement systems as described herein.

[0073] In some embodiments, i) sections are cut from a tissue sample block and transferred to a transfer medium such as tape for subsequent transfer to a slide; ii) the cut sections on the tape are imaged or data is captured by other means; and iii) the data is analyzed to provide a preliminary diagnostic decision.

[0074] In some embodiments, i) sections are cut from a tissue sample block and transferred to a slide; ii) the cut sections on the slide are imaged or data are captured by other means without staining or labeling of the tissue on the slide; and iii) the data are analyzed to provide a preliminary diagnostic decision.

[0075] In some embodiments, i) sections are cut from a tissue sample block in an automated device and transferred to a transfer medium such as tape; ii) the cut sections are transferred from the transfer medium to a slide; iii) the cut tissue sections are imaged or data is captured by other means without staining or labeling of the tissue on the slide; and iv) the data is analyzed to provide a preliminary diagnostic decision.

[0076] According to another aspect of this disclosure, i) prior to being cut from a sample block in an automated apparatus, tissue sections are imaged or data is captured by other means; ii) the data is analyzed to provide a preliminary diagnostic decision; and iii) the sections are then cut from the sample block and transferred to a transfer medium such as tape for transport to slides.

[0077] According to another aspect of the present disclosure, a system is provided which includes one or more imaging systems configured to capture images of i) a tissue sample block containing tissue to be embedded in an implanting material, and / or ii) tissue sections on a tape transfer medium (e.g., tape) after being cut from the sample block, and / or iii) tissue sections on a slide, all of which are captured to provide a preliminary diagnosis without staining or other labeling of the tissue sections.

[0078] According to another aspect of the automated system of the present disclosure, an automated tape transfer system is provided, which includes a controller; a support for holding a sample block of tissue to be embedded in an embedded medium; a cutting device configured to cut tissue sections from the sample block; a transfer medium for transporting the cut tissue sections from the sample block; and one or more imaging systems (or other information acquisition devices / systems) configured to capture a first image of at least one of one or more slides containing the cut tissue sections, which is processed to perform a preliminary diagnosis without staining or labeling of the tissue.

[0079] According to another aspect of the automated system of this disclosure, an automated method is provided for transferring cut tissue sections from a tissue sample block and providing a preliminary diagnosis of the tissue sections without tissue staining or labeling. The automated method is

[0080] a) Steps to advance the tissue section transport medium in an automated system,

[0081] b) i) the block face of a sample block, or ii) a tissue section from the block face, or iii) a transport medium for carrying the tissue section, or iv) one or more slides containing the tissue section, to illuminate, increase contrast, and enhance the distinction of the tissue from the embedded material.

[0082] c) For preliminary diagnosis of tissue sections without tissue staining or labeling, the step of taking an image of one or more of the following: i) the block plane of the sample block, or ii) the cut tissue section from the block plane, or iii) the transport medium carrying the cut tissue section, or iv) one or more slides containing the cut tissue section. Includes.

[0083] Diagnostic decisions can be made by human and / or machine analysis. In some embodiments, a preliminary diagnosis can be performed by a pathologist analyzing images sectioned by a microtome, and the pathologist determines whether additional sections need to be taken. In some embodiments, in an automated system, a preliminary diagnosis can be performed by a pathologist analyzing images during the automated sectioning / tape transfer process of the automated system, and the pathologist determines whether additional sections need to be taken. In other embodiments, a preliminary diagnosis can be performed by an automated device analyzing images during the automated sectioning / tape transfer process of the automated system and providing information to the laboratory, and / or automatically initiating an action in response to the information determined in the preliminary diagnosis, for example, by automatically taking additional sections. In some embodiments, a preliminary diagnosis can be performed by both a pathologist and a machine / device.

[0084] The automated system may include a computer system for collecting and analyzing imaging data acquired by imaging system 2. The imaging data may be stored for later analysis or comparison, if desired. The computer system may have a decision algorithm for determining (in binary analysis) whether images from block planes, tapes, or slides show tissue abnormalities.

[0085] Figure 14 presents an exemplary method for determining whether a tissue section has one or more abnormalities (by either a diagnostic algorithm for the presence or absence of disease or a quality control algorithm for the presence or absence of defects or quality control problems). In step 1402, the system can first illuminate the tissue section using an illumination system. In step 1404, imaging analysis is performed, for example, using an imaging system, to obtain imaging data showing one or more images of the illuminated tissue section. The tissue section can be illuminated using light of an appropriate wavelength of one or more, e.g., visible, UV, etc. In some embodiments, the imaging data shows one or more images taken at different magnification levels from macroscopic images to microscopic images, and can be captured at different wavelengths, for example, to detect fluorescence of different substances. For example, as shown in Figure 15, a tissue sample 1502 in a tissue section 1501 can be illuminated with UV light, so that the tissue sample fluoresces, and thus an image of the tissue sample can be taken. As discussed above, this process can be carried out when the tissue section is on a tissue block, a transfer medium, or a slide 1500, or a combination thereof.

[0086] In some embodiments, imaging data may be fed into a computer system or network and machine learning algorithms in step 1406. In step 1406, a diagnostic analysis may be performed based on one or more biomarkers detected in the tissue. A variety of biomarkers, including but not limited to cells, proteins, molecules, elements, compounds, and other substances that may indicate the presence or absence of a disease or condition, may be used for the diagnostic analysis. In some embodiments, the presence or absence of a disease or condition may also be determined based on a visual observation of the tissue sample. In non-limiting embodiments, based on the received images, cancerous tissue may be determined based on biomarkers such as ER, PR, HER(2) indicating breast cancer, ROS1, p40 indicating lung cancer, SOX 10, and anti-Mart-1 indicating skin cancer. In some embodiments, the diagnostic analysis may include a toxicological analysis of the tissue sample. In addition, or alternatively, in step 1410, imaging data may be examined for quality control purposes. In some embodiments, the quality control step 1410 can be used to determine whether the tissue sample in the tissue section is large enough, intact, or otherwise of sufficient quality for analysis.

[0087] In some embodiments, instead of, or in addition to, digitally analyzing the imaging data by a computer system, the imaging data (e.g., as digital images or printouts) can also be provided to a human user, such as a pathologist. In some embodiments, one or more images generated in the pathology system of this disclosure can be analyzed by themselves or in conjunction with histological image data collected outside the pathology system. In some embodiments, images from the optical reaction measurement system of this disclosure can be viewed directly (on a computer) by a pathologist to assist in the diagnostic process. Algorithmic computer analysis may also be provided to the pathologist to provide them with supporting input.

[0088] In step 1412, based on the analysis of the captured images, the computer system or a human user may provide feedback to the pathology system, individually or together, to update the tissue processing protocol. For example, the microtome may be instructed to cut additional tissue sections. In some embodiments, the thickness of the tissue sections may be adjusted. In some embodiments, the images may be used to determine whether the tissue has been sectioned sufficiently deeply or whether deeper sections are required. In some embodiments, the images may be used to determine whether a significant portion of the tissue is missing or whether the tissue sections need to be taken from different sections of a tissue block. In some embodiments, the images may be used to order one or more specific dyes. For example, a tissue sample is typically stained with H&E for pathology, but if a certain biomarker is detected, other less standard tests (IHC or special dyes) may be requested.

[0089] In some embodiments, as depicted in flowchart 1400 of Figure 14, the decision algorithm can be implemented using a machine learning algorithm. The machine learning algorithm can be trained to assist in the initial diagnosis of a sample. In some embodiments, the machine learning algorithm can be trained using validated training data (e.g., images of cancerous tissue or problems with quality issues). The validated training data can be obtained by human-validated data to ensure the accuracy of the model. For example, the machine learning algorithm may be provided with images of tissue or tissue samples with biomarkers indicating breast cancer, lung cancer, or skin cancer. The machine learning algorithm may be configured to recognize patterns in various input images. With sufficient input data related to historical images, the machine learning algorithm can yield a trained model capable of receiving images from the pathology system and identifying various biomarkers or quality control problems. For example, based on the received images, the machine learning algorithm can diagnose the tissue being processed, for example, based on biomarkers identified in the tissue sample.

[0090] This method and system utilize machine learning to detect whether tissue exhibits disease or condition, or has quality issues, prior to the staining step. For example, used for quality control, the algorithm can determine whether all tissue components are present in the block or absent in the biopsy, and thus request a new sample before the laboratory conducts time-consuming tests. In some embodiments, the diagnostic algorithm can examine images received from an optical reaction measurement system, identify one or more biomarkers in the tissue sample, and request that additional tissue sections be taken from the tissue block.

[0091] Machine learning algorithms can be implemented using one or more neural networks. Machine learning algorithms may include logistic regression, variational autoencoding, convolutional neural networks, or other statistical techniques used to identify and discriminate AD-related lesions. Machine learning algorithms may also use a priori validated Raman scattering models, other scattering models, or optics-physics models. A neural network may have multiple layers, some of which are defined and some are undefined (or hidden). A neural network is a supervised learning neural network.

[0092] In some embodiments, a neural network may include a neural network input layer, one or more neural network hidden layers, and a neural network output layer. Each neural network layer contains multiple nodes (or neurons). The nodes in a neural network layer are typically connected in series. The output of each node in a given neural network layer is connected to the input of one or more nodes in a subsequent neural network layer. Each node is a logic programming unit that performs an activation function (also known as a transfer function) to transform or manipulate data based on its input, weights (if applicable), and bias factors (if applicable), and produces an output. The activation function of each node yields a specific output in response to a particular input, weight, and bias factor. The input of each node may be a scalar, vector, matrix, object, data structure, and / or a reference to such an item. Each node may store its own individual activation function, weights (if applicable), and bias factors (if applicable), independently of other nodes. In some exemplary embodiments, the determination of one or more output nodes in the neural network output layer can be computed or determined using a scoring function and / or a decision tree function, with previously determined weights and bias factors, as understood in the Art.

[0093] In some embodiments, the end-users of such images and data derived from machine learning algorithms may be any of the following: a tissue technician, a laboratory supervisor, a pathologist, or other specialist. Tissue technicians can rely on this method for rapid turnaround time decision-making and rapid dual quality control, giving them a means to the automated sectioning process. Laboratory supervisors can use the algorithm to ensure that the laboratory process is functioning correctly as planned. Pathologists can use the algorithm to make decisions (number of sections needed, type of dye, etc.) much faster, as they will no longer need to wait for slides to be stained and then presented to them. Thus, the algorithm can create shortcuts in current laboratory workflows and pave the way for digital pathology.

[0094] Any suitable computing system can be used to implement the computing devices and methods / functionality described herein and can be transformed into a specific system for implementing the operations and features described herein through hardware, software, and hardware modifications in a manner significantly exceeding mere software execution on a general-purpose computing device, as will be understood by those skilled in the art. An illustrative embodiment of such a computing device 800 is depicted in Figure 13. Computing device 800 is merely an illustrative embodiment of a suitable computing environment and does not limit the scope of the disclosure in any way. A “computing device” as represented by Figure 13 may include a “workstation,” “server,” “laptop,” “desktop,” “handheld device,” “mobile device,” “tablet computer,” or other computing device, as will be understood by those skilled in the art. Provided that computing device 800 is depicted for illustrative purposes, embodiments of the disclosure may utilize any number of computing devices 800 in any number of different ways to implement a single embodiment of the disclosure. Therefore, embodiments of the present disclosure are not limited to a single computing device 800, nor are they limited to a single type of implementation or configuration of the exemplary computing device 800, as will be understood by those skilled in the art.

[0095] Computing device 800 may include a bus 810 that can be directly or indirectly coupled to one or more of the following illustrative components: memory 812, one or more processors 814, one or more presentation components 816, input / output ports 818, input / output component 820, and power source 824. Those skilled in the art will understand that bus 810 may include one or more buses such as an address bus, a data bus, or any combination thereof. Furthermore, those skilled in the art will understand that, depending on the intended use and application 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. Therefore, Figure 8 is merely an illustration of an exemplary computing device that may be used to implement one or more embodiments of the present disclosure and does not limit the present disclosure in any way.

[0096] The computing device 800 may include, or interact with, various 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 technologies, CD-ROMs, digital multipurpose discs (DVDs), or other optical or holographic media, magnetic cassettes, magnetic tapes, magnetic disk storage devices, or other magnetic storage devices that may be used to encode information and can be accessed by the computing device 800.

[0097] Memory 812 may include computer storage media in the form of volatile and / or non-volatile memory. Memory 812 may be removable, non-removable, or any combination thereof. Exemplary hardware devices include devices such as hard drives, solid-state memory, optical disk drives, and equivalents. Computing device 800 may include one or more processors that read data from components such as memory 812 and various I / O components 816. Presentation component 816 presents data indications to the user or other devices. Exemplary presentation components include display devices, speakers, printing components, vibration components, and the like.

[0098] The I / O port 818 can enable the computing device 800 to be logically coupled to other devices such as I / O components 820. Some of the I / O components 820 can be integrated into the computing device 800. Examples of such I / O components 820 include microphones, joysticks, recording devices, gamepads, satellite television receiving antennas, scanning devices, printers, wireless devices, networking devices, and equivalents.

[0099] As used herein, the terms “comprises” and “comprising” are intended to be interpreted as comprehensive, not exclusive. As used herein, the terms “exemplary,” “example,” and “exemplifying” are intended to mean “serving as an example, case, or illustration,” and should not be interpreted as indicating or not indicating a configuration that is preferable or advantageous to other configurations. As used herein, the terms “about,” “generally,” and “approximately” are intended to cover variations that may exist at the upper and lower limits of subjective or objective ranges of values, such as variations in properties, parameters, size, and dimensions. In one non-limiting embodiment, the terms “about,” “generally,” and “approximately” mean being at that value, or +10 percent or less, or -10 percent or less. In one non-limiting embodiment, the terms “about,” “generally,” and “approximately” mean being close enough to be considered included by a person skilled in the art. As used herein, the term “substantially” refers to the complete or near-complete range or degree of an action, characteristic, nature, state, structure, item, or result, as would be understood by those skilled in the art. For example, an object that is “substantially” circular would mean that the object is either perfectly circular to the mathematically determinable limit, or nearly circular as would be recognized or understood by those skilled in the art. The degree of strictly acceptable deviation from absolute perfection may, in some cases, depend on the specific context. However, generally, near-perfect would mean having the same overall result as if absolute and overall perfection had been achieved or obtained. The use of “substantially” is equally applicable when used in a negative sense to refer to the complete or near-complete absence of an action, characteristic, nature, state, structure, item, or result, as would be understood by those skilled in the art.

[0100] While the above description contains many details, these details should not be construed as limitations on the scope of the disclosure, but merely as examples of preferred embodiments. Those skilled in the art will envision many other possible modifications that fall within the scope and spirit of the disclosure. Furthermore, it should be understood that the following claims encompass all general and specific features of the disclosure described herein, and, as a matter of language, all possible terms of the scope of the disclosure that may fall between them.

Claims

1. A system for measuring the optical reaction of tissue samples, wherein the system is A microtome configured to section one or more tissue sections from a tissue block, wherein the one or more tissue sections contain one or more tissue samples, and A transfer medium configured to collect one or more tissue sections and to transfer one or more tissue sections to one or more slides, An optical reaction measurement system comprising: an illumination system configured to illuminate one or more tissue sections; and an imaging system configured to perform imaging analysis on the one or more tissue sections illuminated using the illumination system, wherein the optical reaction measurement system is mounted on a movable stage in the microtome, on the transport medium, or on one or more slides, so that imaging analysis of the one or more tissue sections is performed. A system that includes these features.

2. The lighting system according to claim 1, wherein the lighting system is configured to illuminate one or more tissue sections using structured light.

3. The system according to claim 1, wherein the imaging system is configured to perform the imaging analysis using optical microscopic resolution.

4. The imaging system is the system according to any one of claims 1 to 3, comprising a microscope scanning device.

5. A system for measuring the optical reaction of tissue samples, wherein the system is A microtome configured to section one or more tissue sections from a tissue block for transfer to one or more slides by a transfer medium, wherein the one or more tissue sections contain one or more tissue samples, and An optical reaction measurement system comprising: an illumination system configured to illuminate one or more tissue sections; and an imaging system configured to perform imaging analysis of the one or more tissue sections illuminated using the illumination system, wherein the optical reaction measurement system is mounted on a movable stage in the microtome, on the transport medium, or on one or more slides, so that imaging analysis of the one or more tissue sections is performed. A processor that communicates with the optical reaction measurement system, wherein the processor is programmed to receive imaging data indicating the imaging analysis from the optical reaction measurement system and to determine the presence or absence of one or more abnormalities by presenting the imaging data for the analysis of one or more tissue sections. A system that includes these features.

6. The system according to claim 5, wherein the processor is programmed to determine the presence or absence of one or more abnormalities in the one or more tissue samples of the one or more tissue sections by performing an analysis of the imaging data.

7. The system according to claim 5, further comprising the transfer medium, the transfer medium being configured to collect the one or more tissue sections and to transfer the one or more tissue sections to one or more slides.

8. The system according to claim 5, wherein the one or more abnormalities include the presence of one or more biomarkers indicating a disease in the one or more tissue sections, the presence of one or more quality control problems in the one or more tissue sections, or a combination thereof.

9. The system according to claim 5, wherein the processor is programmed to generate diagnostic values ​​for one or more tissue samples by executing a diagnostic algorithm.

10. The system according to claim 9, wherein the diagnostic value indicates the presence or absence of a disease.

11. The system according to claim 10, wherein the processor is further programmed to obtain one or more additional tissue sections if the diagnostic value indicates the presence of the disease.

12. The system according to any one of claims 5 to 11, wherein the processor is configured to identify one or more biomarkers indicating a disease in one or more tissue samples from the imaging data, and to assign diagnostic values ​​for one or more tissue samples based on the one or more biomarkers.

13. The system according to any one of claims 5 to 11, wherein the processor is programmed to identify one or more quality control problems by executing a quality control algorithm.

14. The lighting system according to any one of claims 5 to 11, wherein the lighting system is configured to illuminate one or more tissue sections using structured light.

15. The imaging system according to any one of claims 5 to 11, wherein the imaging system is configured to perform the imaging analysis using optical microscopic resolution.

16. The system according to any one of claims 5 to 11, wherein the imaging data includes one or more images of one or more tissue sections.

17. The system according to any one of claims 5 to 11, wherein the processor is configured to present the imaging data to a human user as one or more images of one or more tissue sections.

18. A system for measuring the optical reaction of tissue samples, wherein the system is A microtome configured to section one or more tissue sections from a tissue block, wherein the one or more tissue sections contain one or more tissue samples, and A transfer medium configured to collect one or more tissue sections and to transfer one or more tissue sections to one or more slides, An optical reaction measurement system comprising: an illumination system configured to illuminate one or more tissue sections; and an imaging system configured to perform imaging analysis on the one or more tissue sections illuminated using the illumination system, wherein the optical reaction measurement system is mounted on a movable stage in the microtome, on the transport medium, or on one or more slides, so that imaging analysis of the one or more tissue sections is performed. A processor, the processor is programmed to receive imaging data indicating the imaging analysis from the optical reaction measurement system, perform analysis of one or more tissue samples for one or more biomarkers indicating a disease, and, if one or more biomarkers are detected, cause the microtome to section one or more additional tissue sections. A system that includes these features.

19. The system according to claim 18, wherein the processor is programmed to determine the presence or absence of one or more abnormalities in the one or more tissue samples of the one or more tissue sections by performing an analysis of the imaging data.

20. The system according to claim 19, wherein the one or more abnormalities include one or more biomarkers indicating a disease, a quality control problem, or a combination thereof.

21. The system according to claim 18, wherein the processor is programmed to generate diagnostic values ​​for one or more tissue samples by executing a diagnostic algorithm.

22. The system according to claim 21, wherein the diagnostic value indicates the presence or absence of a disease.

23. The system according to claim 22, wherein the processor is further programmed to obtain one or more additional tissue sections if the diagnostic value indicates the presence of the disease.

24. The system according to any one of claims 18 to 23, wherein the processor is configured to identify one or more biomarkers indicating a disease in one or more tissue samples from the imaging data, and to assign diagnostic values ​​for one or more tissue samples based on the one or more biomarkers.

25. The system according to any one of claims 18 to 23, wherein the processor is programmed to identify one or more quality control problems by executing a quality control algorithm.

26. The lighting system according to any one of claims 18 to 23, wherein the lighting system is configured to illuminate one or more tissue sections using structured light.

27. The imaging system according to any one of claims 18 to 23, wherein the imaging system is configured to perform the imaging analysis using optical microscopic resolution.

28. The system according to any one of claims 18 to 23, wherein the imaging data includes one or more images of one or more tissue sections.

29. The system according to any one of claims 18 to 23, wherein the processor is configured to present the imaging data to a human user as one or more images of one or more tissue sections.

30. A method for measuring the optical reaction of a tissue sample, wherein the method is The process of sectioning one or more tissue sections from a tissue block using a microtome, wherein each of the one or more tissue sections contains one or more tissue samples. Transferring one or more tissue sections from the microtome to one or more slides using an automated transfer medium, The illumination system of the optical reaction measurement system illuminates one or more tissue sections, The imaging system of the optical reaction measurement system collects imaging data for one or more tissue sections illuminated by the illumination system by performing imaging analysis. Includes, The optical reaction measurement system is mounted on a movable stage in the microtome, such that imaging analysis of one or more tissue sections is performed on the automated transfer medium or on one or more slides.

31. The method according to claim 30, further comprising presenting the imaging data to one or more users as one or more images of one or more tissue sections.

32. The method according to claim 30, further comprising presenting one or more images of the one or more tissue samples to a human user after the tissue samples have been stained.

33. The method according to any one of claims 30 to 32, further comprising: a processor receiving imaging data indicating the imaging analysis; and the processor analyzing the tissue samples to determine the presence or absence of one or more abnormalities in the one or more tissue samples.

34. The method according to claim 33, further comprising the processor generating diagnostic values ​​for one or more tissue samples indicating the presence or absence of disease in one or more tissue samples by executing a diagnostic algorithm, and presenting the diagnostic values ​​to a human user along with one or more images of the one or more tissue sections.

35. The method according to claim 33, further comprising the processor generating diagnostic values ​​for one or more tissue samples indicating the presence or absence of a disease by executing a diagnostic algorithm.

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