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EP-4737978-A1 - CONTROLLER FOR A LASER MICRODISSECTION SYSTEM, LASER MICRODISSECTION SYSTEM, AND METHOD FOR LASER MICRODISSECTION

EP4737978A1EP 4737978 A1EP4737978 A1EP 4737978A1EP-4737978-A1

Abstract

A controller (136) for a laser microdissection system (100) is configured to receive a first image (300) of a sample (102) comprising multiple image tiles (302) stitched together, and a first set of coordinates in a coordinate system of the first image (300). The first set of coordinates define at least one segment (304) to be removed from the sample (102). The controller (136) is also configured to control the laser microdissection system (100) to generate at least one second image (400) of a part of the sample (102), to generate at least one second set of coordinates in the coordinate system of the second image (400), each of the second sets of coordinates corresponding to at least a subset of the first set of coordinates, and to control the laser microdissection system (100) based on the at least one second set of coordinates to remove the at least one segment (304) from the sample (102). The controller (136) is further configured to determine at least two reference points on the sample (102) visible in the first image (300) and the at least one second image (400), to determine original coordinates corresponding to coordinates of the reference points in the coordinate system of the first image (300), to determine target coordinates corresponding to coordinates of the reference points in a coordinate system of the at least one second image (400), and to generate the at least one second set of coordinates based on the original coordinates and the target coordinates.

Inventors

  • SCHLAUDRAFF, FALK
  • Marr, James
  • GREB, CHRISTOPH
  • HOFFMANN, FLORIAN

Assignees

  • Leica Microsystems CMS GmbH

Dates

Publication Date
20260506
Application Date
20241030

Claims (15)

  1. A controller (136) for a laser microdissection system (100), wherein the controller (136) is configured to receive a first image (300) of a sample (102) comprising multiple image tiles (302) stitched together, and a first set of coordinates in a coordinate system of the first image (300), the first set of coordinates defining at least one segment (304) to be removed from the sample (102); to control the laser microdissection system (100) to generate at least one second image (400) of a part of the sample (102); to generate at least one second set of coordinates in the coordinate system of the second image (400), each of the second sets of coordinates corresponding to at least a subset of the first set of coordinates; and to control the laser microdissection system (100) based on the at least one second set of coordinates to remove the at least one segment (304) from the sample (102); wherein the controller (136) is configured to determine at least two reference points on the sample (102) visible in the first image (300) and the at least one second image (400), to determine original coordinates corresponding to coordinates of the reference points in the coordinate system of the first image (300), to determine target coordinates corresponding to coordinates of the reference points in a coordinate system of the at least one second image (400), and to generate the at least one second set of coordinates based on the original coordinates and the target coordinates.
  2. The controller (136) according to claim 1, wherein the controller (136) is configured to control the laser microdissection system (100) to generate at least two second images (400), each second image (400) comprising a different part of the sample (102), and to determine for each second image (400) at least one of the reference points such that said reference point is visible in the first image (300) and the respective second image (400).
  3. The controller (136) according to claim 1 or 2, wherein the controller (136) is configured to control the laser microdissection system (100) to generate at least two second images (400), each second image (400) comprising a different part of the sample (102), to determine for each of the second images (400) at least two of the reference points such that said reference points are visible in the first image (300) and the respective second image (400), and to generate one of the second sets of coordinates for each of the second images (400).
  4. The controller (136) according to claim 3, wherein the controller (136) is configured to control the laser microdissection system (100) based on one of the second sets of coordinates to remove at least one of the segments (304) from the sample (102) before another of the second images (400) is generated.
  5. The controller (136) according to any of the preceding claims, wherein the controller (136) is configured to determine the original coordinates based on the target coordinates, the first image (300), and the second image (400) using an image matching method.
  6. The controller (136) according to any of the preceding claims, wherein the controller (136) is configured to determine a section of the first image (300) corresponding to at least one of the second images (400), and to determine the original coordinates based on the target coordinates and the section of the first image (300).
  7. The controller (136) according to any of the preceding claims, wherein the laser microdissection system (100) is configured to generate the at least one second image (400) using at least one imaging technique; and wherein the controller (136) is configured to generate an artificial first image (300) based on the first image (300), the artificial first image (300) simulating visual characteristics of the at least one imaging technique, and to determine the original coordinates based on the target coordinates and the artificial first image (300).
  8. The controller (136) according to any of the preceding claims, wherein the controller (136) is configured to determine a coordinate transformation from the coordinate system of the first image (300) to the coordinate system of the at least one second image (400), and to generate the at least one second set of coordinates based on the coordinate transformation.
  9. A laser microdissection system (100), comprising at least one laser light source (110) configured to generate a laser beam, an optical system (112) configured to guide the laser beam onto the sample (102), and the controller (136) according to any one of the preceding claims.
  10. The laser microdissection system (100) according to claim 9, comprising a scanning unit (128) configured to move the laser beam within a field of view of an objective lens (116) of the optical system (112).
  11. The laser microdissection system (100) according to claim 9 or 10, comprising a sample positioning unit (134) configured to move the sample (102) relative to an optical axis (O) of an objective lens (116) of the optical system (112).
  12. A method for laser microdissection, comprising: a) receiving a first image (300) of a sample (102) comprising multiple image tiles (302) stitched together, and a first set of coordinates in a coordinate system of the first image (300), the first set of coordinates defining at least one segment (304) to be removed from the sample (102); b) generating at least one second image (400) of a part of the sample (102) using a laser microdissection system (100); c) generating at least one second set of coordinates in the coordinate system of the second image (400), the at least one second set of coordinates corresponding to at least a subset of the first set of coordinates; and d) controlling the laser microdissection system (100) based on the at least one second set of coordinates to remove the at least one segment (304) from the sample (102); wherein the method further comprises determining at least two reference points on the sample (102) visible in the first image (300) and the at least one second image (400), determining original coordinates corresponding to coordinates of the reference points in the coordinate system of the first image (300), determining target coordinates corresponding to coordinates of the reference points in a coordinate system of the at least one second image (400), and generating the at least one second set of coordinates based on the original coordinates and the target coordinates.
  13. The method according to claim 12, wherein the method further comprises generating at least two second images (400) using a laser microdissection system (100), each second image (400) comprising a different part of the sample (102); and determining for each of the second images (400) at least one of the reference points such that said reference point is visible in the first image (300) and the respective second image (400).
  14. The method according to claim 12, wherein steps b) to d) are repeated for different parts of the sample (102).
  15. The method according to any one of the claims 12 to 14, wherein the sample (102) comprises a tissue microarray section.

Description

Technical field The invention relates to a controller for a laser microdissection system, and to a laser microdissection system. The invention further relates to a method for laser microdissection. Background A laser microdissection system uses a laser beam to separate a small portion, called a dissectate, from a specimen. The specimen may be a thin tissue section, for example, that is cut in order to isolate specific cells or other microscopic regions of interest. These regions of interest may be determined in an overview image of the specimen, which has been captured by a slide scanner, for example. In particular, these regions of interest may be determined as a set of coordinates, which define the regions of interest in terms of coordinates in the overview image. In order to be able to use the set of coordinates with the laser microdissection system, the coordinates need to be transformed into a coordinate system used by the laser microdissection system, for example. Summary It is an object to provide a controller for a laser microdissection system, a laser microdissection system, and a method for laser microdissection, which improve upon known systems and methods. The aforementioned object is achieved by the subject-matter of the independent claims. Further embodiments are defined in the dependent claims and the following description. The proposed controller for a laser microdissection system is configured to receive a first image of a sample comprising multiple image tiles stitched together, and a first set of coordinates in a coordinate system of the first image. The first set of coordinates define at least one segment to be removed from the sample. The controller is also configured to control the laser microdissection system to generate at least one second image of a part of the sample, to generate at least one second set of coordinates in the coordinate system of the second image, each of the second sets of coordinates corresponding to at least a subset of the first set of coordinates, and to control the laser microdissection system based on the at least one second set of coordinates to remove the at least one segment from the sample. The controller is further configured to determine at least two reference points on the sample visible in the first image and the at least one second image, to determine original coordinates corresponding to coordinates of the reference points in the coordinate system of the first image, to determine target coordinates corresponding to coordinates of the reference points in a coordinate system of the at least one second image, and to generate the at least one second set of coordinates based on the original coordinates and the target coordinates. The first image may be an overview image of the sample captured by a slide scanner, a multiplex spatial imager, or a fluorescence microscope, for example. The sample may comprise a carrier, for example a membrane arranged in a frame, a microscope slide or a cell-culture dish, and one or more specimen arranged thereon. The actual specimen may only cover a part of the carrier, meaning that the first image may comprise one or more image tiles which do not comprise the specimen. These image tiles are essentially empty and featureless, making it difficult to stitch them together correctly, as pixel rows and pixel columns cannot be correlated exactly. For example, in a fluorescence image, image tiles which do not comprise a part of the actual specimen are black, making it very difficult to correctly align them for stitching. It has been recognized that this may pose a problem when transferring segments defined in a coordinate system of the overview image into a coordinate system used by the laser micro dissection system. For example, fixed reference points arranged at an edge of the carrier are used. There may be many empty image tiles between these fixed points and the actual specimen, which may cause a misalignment of the segments transferred into the coordinate system used by the laser micro dissection system due to incorrect stitching. Even a small misalignment in the order of 1 µm may cause the laser micro dissection system to miss a cell nucleus, for example, that is about 2 µm to 10 µm in size. The proposed controller addresses the issue of a potential misalignment between the coordinate system of the first image, which may be the overview image captured by the slide scanner, and the coordinate system of the second image, which is captured by the laser microdissection system itself, by using dynamic reference points. The reference points may be structures of the actual specimen, for example, which are visible in both the first image and the second image. From the coordinates of reference points in the first image, i.e. the original coordinates, and the coordinates of reference points in the second image, i.e. the target coordinates, the controller determines a relationship between the coordinate system of the first image and th