US-20260126389-A1 - DEVICES AND METHODS FOR MEASURING BIOLOGICAL SAMPLE TOPOLOGY

Abstract

Disclosed herein, inter alia, are systems and methods for analyzing tissue thickness and structure.

Inventors

• Austin Corbett
• Yuji Ishitsuka
• Robert James Stover

Assignees

• Singular Genomics Systems, Inc.

Dates

Publication Date

20260507

Application Date

20251104

Claims (18)

1. 1 . A method of measuring a tissue topology, the method comprising: distributing a first plurality of fluorescent particles across a first surface of a first solid support; adhering a tissue sample to the first solid support; attaching a second solid support to the first solid support; introducing a solution to the second solid support wherein solution includes a second plurality of fluorescent particles that adhere to an exposed region of the tissue sample; iteratively acquiring images of the first plurality of fluorescent particles and the second plurality of fluorescent particles across a cross section of the tissue sample.
2. 2 . The method of claim 1 , further comprising obtaining an image of the tissue sample.
3. 3 . The method of claim 1 , wherein the images of the first plurality of fluorescent particles and the second plurality of fluorescent particles are acquired using an objective lens that moves along a z axis at defined steps focused on the first plurality of fluorescent particles and/or the second plurality of fluorescent particles.
4. 4 . The method of claim 3 , wherein the images are acquired across an entire cross section of the tissue sample and across an entire surface area of the tissue sample.
5. 5 . The method of claim 1 , wherein introducing a solution to the second solid support comprises flowing a solution through at least one channel of the second solid support.
6. 6 . The method of claim 5 , wherein the solution is introduced into the at least one channel via at least one port of the second solid support.
7. 7 . The method of claim 1 , further wherein the first plurality of fluorescent particles attach to the tissue sample.
8. 8 . The method of claim 1 , wherein the first solid support is a sample slide.
9. 9 . The method of claim 1 , wherein the first plurality of fluorescent particles includes focusing beads.
10. 10 . The method of claim 1 , wherein adhering a tissue sample to the first solid support comprises adhering the tissue sample to a resist positioned on the first surface of the first solid support.
11. 11 . The method of claim 1 , wherein a top of the first solid support corresponds to an interface between the tissue sample and the first solid support, and the bottom of the first solid support corresponds to an interface between tissue section and the second solid support.
12. 12 . The method of claim 1 , further comprising obtaining the tissue sample by cutting a region of tissue with a cutter of a punch device such that the tissue sample is retained within the cutter.
13. 13 . The method of claim 12 , further comprising placing the cutter with the tissue sample onto a receiving array.
14. 14 . The method of claim 13 , further comprising aligning the first solid support to the receiving array.
15. 15 . The method of claim 14 , wherein adhering a tissue sample to the first solid support comprising using a plunger to push the tissue sample out of the cutter onto the first solid support.
16. 16 . The method of claim 15 , further comprising heating the receiving array, the plunger and the first solid support.
17. 17 . The method of claim 16 , further comprising removing the removing the receiving array, the piston, and the plunger from the first solid support such that the tissue sample is retained on the first solid support.
18. 18 . A method of measuring a tissue sample attached to a solid support, the method comprising: positioning the solid support on a sample stage of a device comprising an imaging system; detecting, with the imaging system, a first focal position at a first interface of the tissue sample; detecting, with the imaging system, a second focal position at a second interface of the tissue sample; determining, by the imaging system, a thickness of the tissue sample based on a displacement between the first focal position and the second focal position.

Description

CROSS-REFERENCES TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Application No. 63/716,357, filed Nov. 5, 2024, which is incorporated herein by reference in its entirety and for all purposes. BACKGROUND For many biological applications (e.g., spatial transcriptomics) it is necessary to prepare samples of biological tissues. This preparation includes both the sectioning of larger tissue samples into small, discrete, sections as well as adhering these sections onto a slide such that it can interface with a microscope. It is often useful, if not imperative, to understand the topography of the biological sample including local (micro-folds, voids, etc.) and global (overall thickness, gradients, etc.) structures. Disclosed herein, inter alia, are solutions to these and other problems in the art. BRIEF SUMMARY In an aspect is provided a non-transitory computer-readable medium storing instructions that, when executed by a processor, perform a method for analyzing a tissue sample, the method including obtaining a first image of an tissue sample using a detection apparatus; obtaining a second image of the tissue sample using the detection apparatus; identifying, by one or more processors, a first plurality of positions corresponding to a plurality of fluorescent particles in the first image, and a second plurality of positions corresponding to a plurality of fluorescent particles in the second image; and computationally determining the distance between the first image and the second image. In embodiments, computationally determining the distance includes subtracting a distance from the first plurality of positions and the second plurality of positions. In an aspect is a method of measuring a tissue sample attached to a first solid support, the method including: distributing a first plurality of fluorescent particles across a first surface of a first solid support; adhering a tissue sample to the first solid support; attaching a second solid support to the first solid support; introducing a solution to the second solid support wherein solution includes a second plurality of fluorescent particles that adhere to an exposed region of the tissue sample; and acquiring images of the first plurality of fluorescent particles and the second plurality of fluorescent particles across a cross section of the tissue sample. In embodiments, the method includes iteratively acquiring images across a plurality of cross sections. In embodiments, the method includes determining the thickness of the tissue sample. BRIEF DESCRIPTION OF THE DRAWINGS FIGS. 1A-1B. FIG. 1A provides a schematic for preparing a composition described herein, wherein the composition includes a first solid support including a plurality of a first fluorescent particle attached to the first solid support, a tissue section immobilized to the first solid support, a plurality of a second fluorescent particle, and a second solid support. A sample slide (e.g., a first solid support as described herein) is prepared, wherein the slide includes a resist as described herein. A plurality of focusing beads (e.g., a plurality of first fluorescent particles as described herein) is distributed across the surface of the resist as shown in step 2 of FIG. 1A. Following the deposition of the plurality of the first fluorescent particle at the optimal density, a tissue section as described herein is adhered onto the first solid support, followed by the affixing the second solid support onto the first solid support (as shown in steps 3 and 4 in FIG. 1A), wherein the second solid support includes drilled ports and/or fluidic channels. After affixing the second solid support to the first solid support, a solution including a plurality of the second fluorescent particle as described herein is pushed through the channel of the second solid support to facilitate adherence of the second fluorescent particle to exposed regions of the tissue section (as shown as step 5 of FIG. 1A). Alternatively, in embodiments, after adhering the tissue section onto the first solid support, a solution including a plurality of the second fluorescent particle as described herein is introduced to facilitate adherence of the second fluorescent particle to exposed regions of the tissue section. FIG. 1B provides the orientation of the tissue slide including the plurality of the first fluorescent particle and the plurality of the second fluorescent particle. The top of the tissue slide corresponds to the interface between the tissue section and the first solid support, and the bottom of the tissue slide corresponds to the interface between tissue section and the second solid support. FIG. 2 illustrates a punch device used to cut out a region of tissue with desired characteristics to be used with the composition, systems, and methods described herein (e.g., shown as step 3 in FIG. 1A). The cutter portion of the punch provided in FIG. 2 is removed, flipped, and placed in a receiving arr