Automated method of dissecting biological material

Abstract

An automated method of dissecting biological material from a region of interest (30) within a tissue sample placed on a planar substrate using a dissecting tool comprising an internal cavity and a blade (125) disposed at an inlet of the internal cavity. The method comprises the following steps: identifying the boundary of the region of interest; the method includes identifying a boundary of a blade in a planar substrate, calculating a scraping path of the blade based on the identified boundary, the scraping path causing the blade to engage and scrape off all materials in the ROI, and controlling a position of the anatomical tool relative to the planar substrate such that the blade follows the calculated scraping path, where the calculated scraping path includes one or more individual scraping movements, wherein a knife (125) is pressed onto the planar substrate at a starting position (61, 62) within the identified boundary and moved forward through the ROI until reaching a stop position (71, 72) and raised away from the planar substrate. The method further includes calculating a skiving path such that a stop position of each individual skiving motion is positioned in the skived area within the identified boundary.

Description

Technical Field

[0001] The present invention relates to an automated method for dissecting biological material from a sample placed on a planar substrate (such as a glass slide) using a dissecting tool having a scraper and a tool body in which the scraped material is collected during dissection. Background Art

[0002] Such a method and an apparatus for performing the method are known from WO202054250. The position of the dissecting tool relative to the sample is controlled so that the scraper selectively engages with the material in the identified region of interest (ROI). The knife is brought into contact with a glass slide and is pushed forward through the biological material in the ROI, thereby scraping off the material and collecting it in the tool. Another embodiment is disclosed in WO2022063695, wherein the knife is arranged at the orifice, and suction is applied during dissection so that the sample material separated via scraping is sucked into the orifice and lumen of the tool, wherein the sample material is collected at the bottom side of the filter element across the lumen. Then, the sample material is transferred to the collection tube by arranging the tube around the tool orifice in an airtight manner and generating a pressure pulse that discharges the material into the tube.

[0003] In order to optimize the quality of subsequent analysis, it is important to collect only material from the ROI and not leave ROI material on the glass slide. The ROI material must be broken up so that it can be collected into the tool lumen. At the end of the scraping movement, the knife is raised from the slide. Any scraped material that is still connected to the material on the slide at the position where the knife is raised will be pulled out of the lumen. The inventors have found that when suction is used, by applying a sufficiently large suction force during the dissection, the breakage can be ensured. However, this has the disadvantage of increasing the adhesion of the collected material at the bottom side of the filter, making it more difficult to reliably discharge the material into the collection tube.

[0004] Therefore, there is still room for improvement in defining a scraping method that overcomes the problem of sample material being left behind on the slide without requiring high suction forces. Summary of the invention

[0005] The present invention resides in an automated method for dissecting biological material from a region of interest (ROI) in a sample placed on a planar substrate using a dissecting tool having a scraper arranged at the opening of a lumen in the tool, the scraped material being collected in the tool during dissection. The method comprises the following steps:

[0006] ● Identify the boundaries of the region of interest;

[0007] ● Based on the identified boundaries, calculating a scraping path for the scraper that will cause the blade to engage with and remove all material within the ROI; and

[0008] ● The position of the dissecting tool relative to the planar base is controlled so that the scraper follows the calculated scraping path.

[0009] The scraping path comprises one or more individual scraping movements in which the knife is pressed onto the planar substrate at a starting position within or on the identified boundary and is moved forward through the ROI until a stop position is reached and it is lifted off the planar substrate. According to the invention, the scraping path is calculated so that the stop position of each individual scraping movement is positioned in the scraped area within the identified ROI boundary.

[0010] In one embodiment, the calculated scraping path includes at least one scraping motion that scrapes the identified ROI boundary. In one embodiment, this is the first scraping motion. The knife has a leading edge that is moved forward during dissection to scrape material from a planar substrate (e.g., a glass slide). The knife also has an inner edge and an outer edge that cuts a scraping path that runs through the sample material. When scraping the ROI boundary, the position of the knife is controlled so that the outer edge of the knife is used to cut off the material at the ROI boundary from the adjacent sample material. The knife is along the identified ROI boundary and creates the first scraping path. The knife is raised only after it has returned to and traveled beyond the starting position so that the stop position is positioned on the first scraping path, i.e., positioned on the scraped portion of the ROI boundary.

[0011] Suitably, the dissecting tool is mounted to a tool holder on a dissecting apparatus for performing the method so as to be rotatable about a vertical axis of rotation perpendicular to the glass slide on which the sample is placed. Preferably, the vertical axis of rotation coincides with the outer edge of the scraper. As will be appreciated, the apparatus is further provided with actuators capable of controlling movement of the knife in the x-direction and the y-direction relative to the planar substrate during scraping, wherein one of the actuators allows the knife to be lowered and raised.

[0012] In an automated method of dissection, precision is very important, but optimization of speed and efficiency is also desirable. It may be thought that the most efficient solution is to raise the knife just before it has returned to the starting position, where the remaining distance will be less than the width of the knife, leaving a small unshaved patch. This can then be shaved by rotating the knife so that the leading edge of the knife faces the inner area of ​​the ROI, and then starting the subsequent shaving motion at the unshaved portion of the identified ROI boundary.

[0013] As mentioned above, when the knife is raised, this creates a risk of material being pulled out of the tool lumen. Furthermore, the inventors have found that during scraping, material is pushed forward by the leading edge of the scraper, which, although thin (e.g., 0.03 mm to 0.1 mm), has a greater thickness than the thickness of a typical tissue sample of 0.003 mm to 0.01 mm. If the knife is raised before reaching the scraped area, this material pushed forward will also be left behind, resulting in a more imprecise scraping process.

[0014] Possibly in a first scraping movement, after the border has been scraped, the inner area of ​​the ROI can then be scraped in several subsequent scraping movements, in which the knife is brought into contact with the glass slide at the starting position on the first scraping line created and is moved inwards until a stop position is reached at a different area of ​​the first scraping line.

[0015] In the above embodiment, the first scraping motion of the determined scraping path creates a first scraping line, the outer contour of which coincides with the ROI boundary.

[0016] In an alternative embodiment, the first scraping motion is started in an inner region within the identified ROI boundary, which can be advantageously applied when the tissue sample has a high tear strength and exhibits flaking during scraping. Flaking can occur in the case of paraffin-embedded samples, where the tumor tissue has a high density and the paraffin embedding is locally incomplete. Therefore, when the scraper is pushed forward through the sample material, the tissue sample can tear at relatively weak points instead of being precisely severed from the adjacent material by the outer edge of the knife. Therefore, a scraping motion along the outer contour of the ROI boundary may cause the risk of unwanted sample material being collected.

[0017] In an alternative embodiment, the starting position of the first scraping motion is located within the ROI boundary. In one embodiment, the knife is programmed to follow a loop that completely surrounds the inner area within the ROI boundary. As before, the knife is raised only after it has returned to and passed the starting position. In another embodiment, the first scraping motion is programmed to cause the knife to scrape the entire inner area of ​​the ROI, and then rise from the slide at the scraped portion of the aforementioned inner area.

[0018] In subsequent scraping movements, the starting position of the knife is located on the ROI boundary, wherein the knife is oriented substantially parallel to the local contour of the boundary and with the leading edge facing the interior of the ROI. Suitably, the stopping position of each subsequent scraping movement is on the first scraping path or on a previously created scraping path.

[0019] In an embodiment where the first scraping motion defines a circuitous first scraping path enclosing the ROI region, the stop position is positioned on the first scraping path after the circuit has been completed and the knife has returned to the starting position and has passed a predetermined distance from the starting position. Suitably, the predetermined distance is based on the known width of the knife, and in an embodiment where the knife width is 1.0 mm, the predetermined distance is between 20% and 150% of the knife width and is greater than the position tolerance of the knife in the device used. In an embodiment of a typical dissecting device, the position tolerance is 0.1 mm.

[0020] In another refinement, the scraping path comprises a first scraping movement which starts inside the ROI and subsequent scraping movements of the scraping path are calculated only after it has been determined whether the tissue sample to be dissected exhibits exfoliation.

[0021] The apparatus for performing automated dissection according to the invention typically comprises an imaging system, which is used to obtain an image of the slide. The system comprises an imaging sensor, the position of which relative to the scraper is previously calibrated.

[0022] Advantageously, the method may further comprise the steps of capturing an image of at least a portion of the first scraping line created during the first scraping motion; and processing the captured image to determine whether the outer edge / boundary of the created scraping line portion coincides with the programmed path of the knife outer edge. Suitably, the portion of the first scraping line used as a "test line" follows a straight line.

[0023] If it is determined that the boundary of the aforementioned scraped portion has been completely severed from the adjacent material, that is, the scraped line does not contain any sample material, a scraping path is calculated to remove the remaining ROI sample material from the slide, wherein one of the subsequent scraping motions is programmed to scrape the outer contour of the identified ROI boundary, as described for the first embodiment.

[0024] When the result of image processing is that the boundary of the scraped portion deviates from the programmed path of the outer edge of the knife, the calculated scraping path for removing the remaining ROI material includes a subsequent scraping movement in which the knife is positioned on the identified ROI boundary and is oriented parallel to the local contour and moved inward, such as described above.

[0025] Suitably, the step of processing the captured image may include: detecting a boundary of the shaved portion; and comparing the detected boundary to the programmed path, thereby calculating the deviation distance therebetween (if any). A threshold may be set based on a mean absolute deviation (e.g., 0.1 mm) and / or a standard deviation, wherein if the threshold is exceeded, it is determined that the detected boundary deviates from the programmed path.

[0026] The scraping path is calculated based on the identified ROI boundary. Typically, the boundary will include local contour portions that intersect at an angle, and the method includes estimating the length of the intersecting portions and estimating the angle at which they intersect. Advantageously, the scraping path is calculated according to one or more other rules that improve the accuracy of the dissection as well as the speed and efficiency.

[0027] When the scraper is oriented perpendicular to the direction of forward translation, the leading edge of the scraper has a maximum effective width. As the knife moves forward through the ROI material, this creates a scraping line of corresponding width. The effective width can be reduced by changing the angle of orientation of the leading edge of the knife relative to the direction of translation.

[0028] Another rule that can be applied when calculating the scraping path is that the leading edge of the knife is oriented perpendicular to the translation direction unless the knife width exceeds the local width of the ROI. Therefore, the step of calculating the scraping path may include estimating the local width of the ROI to be scraped in a specific scraping movement. When the local width is greater than the maximum knife width, the leading edge of the knife is oriented perpendicular to the translation direction. This maximizes the efficiency of the specific movement. When the estimated local width is narrower than the maximum knife width, the knife is rotated around the vertical axis to adjust the orientation of the leading edge of the knife relative to the translation direction, thereby reducing the effective width as needed.

[0029] Another rule that may be applied is that the knife motion does not stop at the local contour of the identified boundary if the leading edge is parallel to the local contour and is oriented towards the local contour. This prevents the ROI material from being pushed outside the boundary.

[0030] When the identified boundary includes a corner (i.e., a first local contour portion and a second local contour portion intersecting at an angle of 95 to 100 degrees or less), the angle of intersection is estimated. In an embodiment in which the boundary of the ROI is scraped using the outer edge of the knife, another rule that can be applied when calculating the associated scraping motion of the scraping path is that before reaching the corner, the knife rotates backward around a vertical rotation axis coinciding with the outer edge. As mentioned above, the default orientation angle of the knife relative to the first local contour portion of the ROI boundary is 90 degrees, i.e., the leading edge is perpendicular to the first local contour portion. Suitably, the forward movement of the knife is terminated before the inner edge of the knife reaches the second local contour portion, and before continuing to move forward, the angular orientation of the knife relative to the first local contour portion is adjusted to be less than the estimated angle of the corner.

[0031] Advantageously, subsequent scraping motions of the calculated scraping path create straight and mutually parallel scraping lines. This helps to optimize the speed and efficiency of the dissection process. To improve accuracy, the scraping path can be determined so that adjacent scraping routes slightly overlap each other, for example by 5% to 20% of the line width. In another improvement, the method may include identifying a direction in which the region of interest has a maximum length, or a local contour portion of the ROI boundary has a maximum length in the direction. The scraping path is then calculated so that parallel scraping routes are performed in the identified maximum length direction.

[0032] The scraper of the dissecting tool used in the method of the present invention has a straight leading edge with a width of, for example, 1.0 mm. Any of the dissecting tools disclosed in WO2022063695 can be used in the method of the present invention, and the content of this document is incorporated by reference. The disclosed tool includes a filter element that spans the lumen so that the scraped ROI material drawn into the tool is captured at the bottom side of the filter element. The scraped material is transferred to a collection tube by arranging the tube around the end of the dissecting tool in an airtight manner and generating a pressure pulse that discharges the material.

[0033] Preferably, the transfer is performed after all ROI material has been scraped from the slide. Depending on the size of the ROI, it may happen that the filter becomes slightly blocked before all material has been collected, which reduces the effectiveness of suction during dissection. For a specific tool with a filter, a threshold value can be defined to correspond to the surface area of ​​the scraped material that causes a risk of blockage. The scraped surface area is determined by the known width of the knife and the length of travel during scraping. A corresponding threshold value can be determined for the length of travel of the knife. When the threshold value is reached, it is beneficial to interrupt the scraping and perform an intermediate transfer action.

[0034] Thus, the method may additionally comprise calculating the travel length of the knife during scraping and, after completion of the scraping movement, interrupting the scraping path when the calculated length reaches a predetermined threshold. The tool is raised only after the knife has entered the scraped area and can be moved, for example, to a collection station, to which the scraped material is transferred. The tool is then returned to the slide and the remainder of the calculated scraping path is performed.

[0035] It will be appreciated by those skilled in the art that two or more of the above-mentioned embodiments, implementations, and / or aspects of the invention may be combined in any way deemed useful. BRIEF DESCRIPTION OF THE DRAWINGS

[0036] The present invention will now be further elucidated with reference to the embodiments described below.

[0037] Figure 1 One embodiment of a tissue sample is shown, the tissue sample comprising a region of interest to be dissected for analysis;

[0038] Figure 2a is a schematic representation of an apparatus for carrying out the automated method of dissection according to the present invention;

[0039] Figure 2b is a cross-sectional side view of one embodiment of a dissection tool engaged with a tissue sample on a slide, the dissection tool being used in the methods of the present invention;

[0040] Figure 2c is a cross-sectional side view of another embodiment of a dissection tool that may be used in the methods of the present invention;

[0041] Figure 3a and Figure 3b The portion of the scraping motion that is inconsistent with the method of the present invention is schematically drawn;

[0042] Figure 4a Shown from Figure 1a tissue sample in which the first scraping movement and the second scraping movement have been performed according to the first embodiment of the method of the present invention;

[0043] Figure 4b and Figure 4c An embodiment of a portion of a ROI boundary including a corner is shown, and different positions of the scraper are plotted when crossing the corner;

[0044] Figure 5 Another embodiment of a ROI boundary including a relatively narrow portion is shown, and different positions of the scraper are plotted before entering the narrow portion, during entering the narrow portion, and after leaving the narrow portion;

[0045] Figure 6 Shown from Figure 1 A tissue sample in which a first scraping movement and a second scraping movement have been performed according to a second embodiment of the method according to the invention.

[0046] It should be noted that items with the same reference numerals in different drawings have the same structural features and the same functions, or are the same symbols. If the function and / or structure of such items have been explained, there is no need to repeat the explanation in the detailed description. DETAILED DESCRIPTION

[0047] Pathological diagnostic studies of biological material, such as tissues and cells, form the basis of many treatment decisions, particularly in oncology. For example, genomic-based tests are performed to inform treatment options for individual patients diagnosed with cancer. Biological material / tissue can be obtained from a biopsy and then, for example, embedded in paraffin and cut into thin slices that are mounted on glass slides. These slices will be referred to as tissue samples. Other methods of obtaining and preparing biological material are known. One embodiment of a tissue sample placed on a glass slide 10 is shown in FIG. Figure 1 Shown in.

[0048] The tissue sample 20 has a region of interest (ROI) 30, which contains material within the boundaries 35 of the ROI to be subjected to diagnostic testing. This material must be physically separated from the slide and from unwanted sample material 25 outside the boundaries. The ROI and associated boundaries 35 can be identified by staining, or a pathologist can provide markings on a reference slide after analysis under a microscope. The ROI can also be identified via processing a digital image of the sample. When the ROI has been identified, the material is removed / dissected from the slide and then transferred to the analysis arrangement. Typically, the material is transferred to a collection tube, after which sample preparation process steps (such as cell lysis, purification and amplification, etc.) and further necessary processing steps are performed. As will be appreciated, the reliability and accuracy of the analysis are optimized by ensuring that only anatomical material from the ROI is present, and by maximizing the amount of the collected ROI material.

[0049] The present invention defines an automated method for dissecting biological material from a ROI within a sample using a tool with a scraper, the ROI being placed on a planar substrate (such as a glass slide), the scraper being pressed onto the slide and being moved forward through the sample, thereby scraping off the ROI material and collecting it in a cavity inside the tool. In a first step, the boundaries of the ROI are identified. Thereafter, based on the identified boundaries, a scraping path for the knife is calculated. The position of the tool relative to the slide is controlled so that the scraper follows the calculated scraping path. In the method of the present invention, the scraping path is calculated according to one or more rules, which are designed to optimize the accuracy of the dissection by ensuring that material from the region of interest is not left behind on the glass slide.

[0050] Figure 2a A schematic arrangement of an apparatus for carrying out the method of the invention is shown.

[0051] The apparatus 100 includes a platform 110 for supporting a glass slide 10, a tissue sample (such as Figure 1 The sample 20 shown in FIG. 1 is placed on the glass slide 10. The apparatus is equipped with a dissection tool 120 having a scraping head / scratcher 125. Preferably, the dissection tool 120 is fixedly connected to a robotic table 130, which includes a series of actuators for performing the necessary movements during the dissection. Suitably, the robotic table 130 includes:

[0052] - a rotary actuator for rotating the tool about a vertical axis R, said vertical axis R being perpendicular to the platform 110;

[0053] -XY stage for translational movement, and

[0054] - Z-table for vertical movement. The Z-table may include hinge bearings for position control to ensure a constant and precise downward force is applied during dissection.

[0055] As will be appreciated, it is also possible that the necessary actuator or actuators are connected to the platform 110 .

[0056] The device also includes an imaging system 150, which is used to identify the boundaries of the ROI. The imaging system includes an imaging sensor, wherein the position of the scraper relative to the sensor is pre-calibrated. The device also includes: a processor, which is used to calculate a suitable scraping path based on the identified boundaries; and a controller 140, which receives the calculated scraping path and controls the robot workbench accordingly so that the scraper of the dissecting tool moves relative to the platform to scrape off all materials within the identified ROI. Preferably, the device is also equipped with a vacuum generator 160, which generates an updraft at the scraper 125 so that the scraped material is sucked into the tool cavity.

[0057] Cross-sectional side view of the tool Figure 2b . The tool 120 in the depicted embodiment comprises: a thin-walled tube having an inner cavity 128; and a scraping head located at the entrance of the inner cavity. The front or leading edge of the tube serves as a scraper 125 of the scraping head. The scraper has a bottom 125a, which is brought into contact with the top surface of the slide 10. The leading edge of the scraper also contacts the tissue sample 20 in the scraping area, which is formed by the bottom 125a of the tube located in the contact area and the opposite side portions 125b, 125c. Therefore, when relative movement occurs in the X direction, material from the tissue sample is scraped off the slide 10 into the cavity 128 of the dissecting tool. In the scraping area, the portion 125b defines the outer edge of the scraper; the portion 125c defines the inner edge of the scraper, wherein the leading edge as a whole behaves as a chisel. The scraping lines (which are cut through the tissue sample 20) have a width w corresponding to the effective width of the scraper between the outer edge 125b and the inner edge 125c in the scraping area.

[0058] Another embodiment of the dissection tool is Figure 2c 220, the dissection tool can be mounted to a dissection device for implementing the method of the present invention. The tool 220 includes a body portion 226 formed by a single component through which the tool lumen extends. The diameter of a portion of the lumen 228 is tapered toward the tool orifice 223. Another portion of the lumen is formed by a tapered recess 450, which is suitable for accurately aligning the tool with a correspondingly shaped tapered protrusion on a tool holder of the dissection device.

[0059] The tool body portion 226 also includes a base 230 for positioning the filter element 229 in the axial direction. The scraper 225 of the tool is arranged in a second portion 227, which is coupled to the body portion 226 and extends at an angle relative to the longitudinal center axis of the tool lumen. In the embodiment depicted, the second portion 427 is overmolded to the scraper 225 and is irreversibly coupled to the body portion 226 via form fit, adhesive bonding or other suitable coupling methods. In other embodiments, the tool body is overmolded to the scraper as a whole.

[0060] The scraping path calculated for a particular scraper and a particular ROI includes several individual scraping movements in which the scraper is brought into contact with the glass slide at a starting position and is moved relative to the slide until it reaches a stop position and is lifted from the slide. As the scraper 125 is moved forward through the ROI material, as Figure 3a As shown, the material can be separated in the form of a ribbon 30a that is introduced into or drawn into the tool lumen during dissection. If the knife is raised while the leading edge of the ribbon 30a is still attached to adjacent sample material, the ribbon of material can be pulled out of the lumen, as shown. Figure 3b During dissection, the front / leading edge of the scraper also pushes sample material forward, which creates an accumulation 30b or "pile" of ROI material in front of the blade. If the accumulation in front of the blade in the scraping path is not taken into account, this material will also be left behind.

[0061] According to the invention, the scraping path is calculated such that each individual scraping movement ends at a scraped position within the identified ROI boundaries.

[0062] In a preferred embodiment, the scraping path starts with a first scraping movement, in which the identified ROI boundary 35 is scraped. Figure 4a , Figure 4a Shown as Figure 1The same tissue sample drawn, the scraper 125 is brought into contact with the slide at a starting position 61 on the identified boundary. Typically, the boundary includes intersecting local contour portions, and one possible way to select the starting position is to identify the longest local contour portion and start at a position on the longest local contour portion. The knife is oriented so that its leading edge is substantially perpendicular to the boundary at that position, and is further positioned so that the outer edge coincides with the outer contour of the boundary. The knife is then moved forward in a first translational movement indicated by arrow a. The knife is then moved along the boundary in several subsequent translational movements, wherein the leading edge remains as perpendicular as possible to the local contour of the boundary, and the outer edge is used to cut the ROI material from the unwanted sample material 25. When crossing a corner at an angle of 95 to 100 degrees or less, a different orientation is typically required, which will be referred to in detail. Figure 4b and Figure 4c describe.

[0063] exist Figure 4a , the knife 125 is shown at different positions in subsequent translations, with the first scraping line 51 being created along the border. In the final translational movement, as indicated by arrow q, the knife returns to the starting position 61, moves over, for example, 50% of the width of the knife, and is lifted from the slide at the stop position 71, which is the area that has been scraped.

[0064] Figure 4b and Figure 4c One embodiment of a ROI boundary is drawn having local contour portions 35a, 35b intersecting at an angle < 90 degrees, thus creating a corner 38. In addition, the knife 125 is shown at several different positions 1-7 as it passes over the corner 38 during a first scraping motion.

[0065] Suitably, the step of identifying the boundary 35 of the ROI includes estimating the angle of any corners within the boundary. In the illustrated embodiment, the corner 38 has an angle of 70 degrees. When approaching a corner and moving forward between positions 1 and 2, the knife 125 is oriented perpendicular to the local contour 35a, and the knife outer edge 125b coincides with the outer edge of the local contour. The forward movement is terminated at position 2, preferably before the inner edge 125c of the knife encounters the local contour 35b. This prevents the accumulation of ROI material (such as Figure 3b) is pushed outside the boundary. The knife is then rotated backward (for example, at an angle of 30 degrees) to position 3 about a vertical rotation axis R (see FIG. 2 ), which coincides with the knife outer edge 125b. At position 3, the knife has an orientation angle θ relative to the local contour portion 35a, which is less than the estimated angle of the corner. It is then moved forward to position 4, where the outer edge is approximately located at the intersection between contour portions 35a and 35b. Figure 4b As shown, the knife then rotates back again to position 5 and then moves forward with the angle adjustment to position 6, wherein the knife is now perpendicular to the local contour 35b and the knife outer edge 125b coincides with the local contour 35b. The knife then moves forward in a straight line to position 7.

[0066] During the individual scraping movements, the knife remains in contact with the slide. Angular adjustments of the knife about the vertical axis of rotation can be made during continuous or stepwise movement, optionally while stopping the linear movement.

[0067] After creating the first scraping line 51, which has an outer contour coinciding with the ROI boundary, the interior 30 of the ROI can then be scraped in several subsequent scraping movements. Figure 4a , the second scraping path 52 can be created by bringing the knife into contact with the slide 10 at a second starting position 62 on the first scraping path 51 and moving the knife forward to a second stop position 72 at the opposite side of the first scraping path. Preferably, the subsequent scraping movements are parallel to each other and may overlap each other slightly, for example by 10% to 20% of the knife width. The number of additional scraping movements depends on the knife width and the size of the area to be scraped.

[0068] The most efficient way to dissect is to move the blade forward with the leading edge perpendicular to the direction of translation so that the blade width is at its maximum. This is not always possible, for example, when negotiating a corner. It may also be necessary to change the blade orientation to account for the local width of the ROI.

[0069] Figure 5Another embodiment of a ROI 530 having a border 535 is shown. A portion of the ROI 530 has a local width s that is narrower than the maximum effective width w of the scraper 125. The knife is again shown at several different positions 1-7 during the scraping motion. As the knife moves from position 1 to position 2, the local width of the ROI>w, and the knife is oriented with the leading edge perpendicular to the direction of translation. The knife rotates backward about a vertical rotation axis that coincides with the outer edge of the knife 125, and when advancing forward to position 3, the orientation angle is further adjusted, thereby reducing the effective width of the knife as the knife enters the narrow portion 535a and advances to position 4. As shown, as the knife further advances to positions 5, 6, and 7, the angle of orientation is adjusted based on the local width of the ROI.

[0070] In general, the most efficient way to scrape a specific ROI is to start from the ROI border and then scrape the inner area in several subsequent scraping movements, as described above for Figure 4a as described. Depending on the type of tissue sample, such as the tissue samples with high tear strength described above, there is a risk of flaking when the outer edge of the knife is used to cut the ROI from adjacent sample material at the ROI boundary. Therefore, it is advisable that a different type of scraping path includes several scraping movements, in which the knife is placed on the ROI boundary, wherein the leading edge is essentially parallel to the local contour and is moved forward towards the inner area of ​​the ROI. When the length of the local contour portion is less than the width of the knife, the knife is not moved forward, but is only pressed down onto the portion, thereby cutting it off from adjacent unwanted material. The severed portion can then be scraped in a subsequent scraping movement, in which the outer edge of the knife follows the local contour.

[0071] According to the invention, each scraping movement ends after it has reached the scraped area, ie the knife is lifted from the glass slide.The first scraping movement of the scraping path is then programmed to start at the inner area of ​​the ROI.

[0072] One embodiment of a possible first scraping line and a second scraping line is Figure 6. The knife is placed on the slide 10 at the starting position 661 inside the identified ROI boundary 635 and is moved forward to create a continuous first scraping line 651, which completely surrounds the area 630a of the ROI material within the boundary. For simplicity, a substantially rectangular scraping line 651 is drawn, although other enclosing geometries are possible. The knife moves in a "counterclockwise" direction until it returns to and passes through the first starting position 661, and is then raised at the stop position 671. In the second scraping movement, the knife is placed at the second starting position 662 on the ROI boundary 635 and is moved forward to create the second scraping line 652. The second scraping movement ends at the stop position 672, which is on a portion of the first scraping line 681. In the subsequent scraping movement, the knife is returned to the new starting position on the ROI boundary and is moved inward until the previously created scraping line is reached. When all ROI material has been collected, the process stops.

[0073] Examples, implementations or optional features (whether or not indicated as non-limiting) should not be construed as limitations on the claimed invention. It should be noted that the above-mentioned embodiments illustrate rather than limit the present invention, and that those skilled in the art will be able to design many alternative implementations without departing from the scope of the appended claims.

[0074] In the claims, any reference signs placed between parentheses shall not be construed as limiting the claim. The use of the verb "comprise" and its variations does not exclude the presence of elements or steps other than those stated in a claim. The article "a" or "an" preceding an element does not exclude the presence of a plurality of such elements. The invention may be implemented by means of hardware comprising several distinct elements, and by means of a suitably programmed computer. In a device claim enumerating several means, several of these means may be implemented by the same item of hardware. The mere fact that certain measures are recited in mutually different dependent claims does not indicate that a combination of these measures cannot be used to advantage.

[0075] Reference numerals

[0076] 1-7 The position of the scraper at different times during the scraping motion

[0077] 10 Glass slides

[0078] 20 tissue samples

[0079] 25 Unwanted tissue material

[0080] 30 Region of Interest (ROI)

[0081] 30a Strips of tissue material dissected in a scraping motion

[0082] 30b Accumulation of tissue material that is pushed forward during the scraping motion

[0083] 35, 535, 635 ROI boundaries

[0084] 35a, 35b Intersection of ROI boundaries

[0085] 38 Corners within ROI boundaries (where multiple parts are at angles ≤ 90 degrees)

[0086] Degree intersection)

[0087] 51, 651 First Scraping Line

[0088] 52, 652 Second scraping line

[0089] 61, 661 Starting position of the first scraping line

[0090] 62, 662 Starting position of the second scraping line

[0091] 71, 671 Stop position of the first scraping line

[0092] 72, 672 Stop position of the second scraping line

[0093] 100 Dissection Equipment

[0094] 110 Platform for supporting glass slides

[0095] 120, 220 Dissection tools

[0096] 125, 225 Dissecting tool scraper

[0097] 125a Bottom of tubular scraper

[0098] 125b Outer edge of scraper

[0099] 125c Inner edge of scraper

[0100] 128, 228 Lumen of dissecting tools

[0101] 130 A device for adjusting the position of the knife relative to the glass slide

[0102] Robot workbench

[0103] 140 Controller

[0104] 150 Imaging System

[0105] 160 Vacuum generator

[0106] 223 Orifice for dissecting tools

[0107] 226 The main part of the dissection tool

[0108] 427 Second tool body

[0109] 229 filter element

[0110] 230 Base for holding filter element

[0111] 530, 630a ROI part

[0112] a The first translation movement of the scraping motion

[0113] q Final translational movement of the scraping motion

[0114] R Vertical rotation axis of the dissection tool

[0115] s Local width of a portion of the ROI

[0116] w Width of scraper / scraping line

[0117] θ The orientation angle of the knife relative to the local contour

Claims

1. An automated method for dissecting biological material from a region of interest (30, 530, 630) within a tissue sample (20) using a dissecting tool (120, 220), the tissue sample (20) being placed on a planar substrate (10), the dissecting tool (120, 220) comprising an inner cavity (128, 228) and a scraper (125) arranged at an entrance of the inner cavity; The method comprises the following steps: ● identifying the boundaries of the region of interest (35, 535, 635); ● calculating a scraping path for the scraper based on the identified boundaries, the scraping path causing the scraper to engage with and scrape away all material in the region of interest, and ● controlling the position of the dissecting tool relative to the planar base so that the scraper follows the calculated scraping path, wherein: The calculated scraping path includes one or more individual scraping movements, in which the knife (125) is pressed onto the planar substrate (10) at a starting position (61, 62, 661, 662) within the identified boundaries and is moved forward through the ROI until it reaches a stop position (71, 72, 671, 672) and is lifted off the planar substrate, characterized in that The scraping path is calculated so that the stop position of each individual scraping movement is located in the already scraped area within the identified boundaries.

2. A method according to claim 1, wherein the dissection tool is mounted so as to rotate about a vertical rotation axis (R), the vertical rotation axis (R) coinciding with the outer edge (125b) of the scraper.

3. A method according to claim 2, wherein the calculated scraping path includes a scraping motion that creates a scraping line (51, 651), the scraping line (51, 651) completely surrounding at least a portion of the area of ​​interest, wherein the position of the knife (125) is controlled along a loop that will return the knife to the starting position (61, 661) and continue through the starting position so that the stop position (71, 671) is positioned on the scraped portion of the created scraping line.

4. The method according to claim 3, wherein the distance between the stop position and the starting position is 20% to 150% of the width of the scraper, and the distance is greater than the position tolerance of the dissection device to which the dissection tool is mounted.

5. The method according to claim 3 or 4, wherein: ● The outer contour of the created scraping line (51) coincides with the identified boundary (35); and ● During the scraping motion, the position of the scraper (125, 225) is controlled so that the outer edge (125b) of the scraper is along the identified boundary (35) and is used to sever material at the boundary from adjacent material (25) of the sample (20).

6. A method according to claim 5, wherein the step of identifying the boundary includes identifying local contour portions (35a, 35b) of the boundary intersecting at a corner (38) and estimating the intersection angle, the corner (38) having an angle of 100 degrees or less, and wherein during the scraping motion, the position of the scraper (125, 225) is controlled so that before reaching the corner (38), the leading edge of the scraper (125, 225) rotates backward about the vertical rotation axis (R) so as to be oriented at an angle (θ) less than the estimated intersection angle.

7. Method according to claim 5 or 6, wherein the scraping movement of the outer edge of the knife along the identified border (35, 535) is a first scraping movement and the interior of the region of interest (30) is scraped in several subsequent scraping movements.

8. The method according to any one of claims 1 to 3, wherein the first scraping motion and the associated first scraping line (651) are located within the identified boundary (625).

9. A method according to claim 8, wherein the calculated scraping path includes several subsequent scraping movements, each of which has a starting position (662) located on the identified boundary, wherein the leading edge of the knife (125, 225) is oriented parallel to the local contour of the boundary (635) at the corresponding starting position, and wherein the knife moves forward toward the interior of the area of ​​interest until reaching a stop position (672), wherein the stop position (672) is located on the first scraping line (651) or on a previously created scraping line.

10. The method according to claim 7 or 9, wherein the subsequent scraping movements create scraping lines (52, 652) parallel to each other.

11. The method according to claim 7, 9 or 10, wherein adjacent scraping lines overlap each other by an amount corresponding to 5% to 20% of the width (w) of the scraper (125).

12. The method according to claim 10 or 11, further comprising: identifying a direction in which the region of interest has a maximum length, or in which a local contour portion of the ROI boundary (35) has a maximum length; And, the scraping path is calculated so that parallel scraping lines are performed in the direction of the identified maximum length.

13. The method according to any preceding claim, wherein the step of calculating the scraping path further comprises: estimating a local width (s) of a region of interest to be scraped in a specific scraping motion; and orienting the leading edge of the scraper (125, 225) perpendicular to the direction of translation unless the width (w) of the blade is smaller than the estimated local (s).

14. The method of claim 8, wherein the dissection tool is mounted to a device comprising an imaging system (150) and a processor, the method further comprising the steps of capturing an image of at least a portion of the first scraping line (651) and processing the captured image, wherein the step of processing comprises: ● detecting a boundary of the first scraping line portion; ● comparing the detected boundary with a programmed path of a corresponding edge (125a, 125b) of the scraper (125, 225); as well as ● determining whether the detected boundary deviates from the programmed path; and wherein if it is determined that a deviation has occurred, - the calculated scraping path comprises several subsequent scraping movements as defined in claim 9, and in other cases, The calculated scraping path comprises a subsequent scraping movement as defined in claim 5 .

15. A method according to any preceding claim, wherein: ● The dissection tool (220) includes a filter element (229) that spans the lumen (228) of the scraping tool; ● The dissection tool is connected to a vacuum generator (160) for creating an updraft at the inlet (223) of the tool cavity, the updraft causing the scraped material to be sucked into the tool and retained at the bottom side of the filter element (229); ● The method comprises the steps of calculating the distance travelled by the scraper (225) during scraping, and ● The method further comprises: interrupting the scraping path after the scraping motion is completed if the calculated distance exceeds a predetermined threshold, wherein the threshold corresponds to the maximum surface area of ​​the sample material, the sample material can be stored at the bottom side of the filter element (229) without adversely affecting the suction performance; and re-enabling the scraping path after the scraped material has been transferred to the collection tube.

16. A dissection device (100), comprising: ● A dissecting tool having an inner cavity (128, 228) and a scraper (125) arranged at the entrance of the inner cavity; ● A platform (110), the platform (110) is used to support a planar substrate (10), and a tissue sample (20) is placed on the planar substrate (10); ● an imaging system (150) for identifying a boundary (35, 535, 636) of a region of interest (30) within the tissue sample; ● a processor for calculating a scraping path that will cause the scraper (125, 225) to engage all sample material within the identified boundaries; ● a series of actuators (130) for moving the dissection tool relative to the platform (110) in the X, Y and Z directions and for rotating the tool about a vertical rotation axis (R); ● A controller (140) for receiving the calculated scraping path and controlling the series of actuators (130) so that the scraper follows the calculated scraping path; Characterized in that the processor is configured to calculate the scraping path so that automated dissection is performed according to the method according to any one of claims 1 to 14.

17. The dissecting device (100) according to claim 16 further comprises a vacuum generator (160) for generating an ascending airflow at an inlet (223) of a tool lumen (228), wherein the tool further comprises a filter element (129) spanning the lumen, wherein the device is configured to perform the method of claim 15.

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