US 12,406,364 B2
Systems and methods for spatial analysis of analytes using fiducial alignment
Dongyao Li, San Jose, CA (US)
Assigned to 10X GENOMICS, INC., Pleasanton, CA (US)
Filed by 10x Genomics, Inc., Pleasanton, CA (US)
Filed on Feb. 14, 2023, as Appl. No. 18/169,132.
Claims priority of provisional application 63/310,242, filed on Feb. 15, 2022.
Prior Publication US 2023/0306593 A1, Sep. 28, 2023
Int. Cl. G06T 7/00 (2017.01); G06T 3/02 (2024.01); G06T 3/20 (2006.01); G06T 7/13 (2017.01); G06T 7/168 (2017.01); G06T 7/33 (2017.01)
CPC G06T 7/0012 (2013.01) [G06T 3/02 (2024.01); G06T 3/20 (2013.01); G06T 7/13 (2017.01); G06T 7/168 (2017.01); G06T 7/337 (2017.01); G06T 2207/10056 (2013.01); G06T 2207/30024 (2013.01); G06T 2207/30204 (2013.01)] 20 Claims
OG exemplary drawing
 
1. A method of spatial analysis of analytes comprising:
A) obtaining a data structure in electronic form comprising an image of a sample on a substrate, wherein:
the substrate includes a plurality of border regions, wherein each respective border region in the plurality of border regions intersects another border region in the plurality of border regions,
the substrate includes at least a first plurality of fiducial markers,
the first plurality of fiducial markers comprises at least three fiducial markers,
each respective fiducial marker in the first plurality of fiducial markers encodes a different N-digit code, in a plurality of N-digit codes, wherein N is an integer greater than 3,
at least two different border regions in the plurality of border regions includes a respective fiducial marker in the first plurality of fiducial markers,
the substrate includes a set of capture spots, wherein the set of capture spots comprises at least 1000 capture spots, and
the image comprises a plurality of pixel values, each respective pixel value in the plurality of pixel values corresponding to a pixel in an array of pixels, wherein the array of pixels comprises at least 100,000 pixels;
B) analyzing the plurality of pixel values to identify a respective location of each fiducial marker in the first plurality of fiducial markers within the image;
C) aligning the respective location of each fiducial marker in the first plurality of fiducial markers within the image with a location of each reference fiducial marker in a plurality of reference fiducial markers of a first template using an alignment algorithm to obtain a final transformation between the first plurality of fiducial markers of the image and the plurality of reference fiducial markers of the first template;
D) using the final transformation and a coordinate system of the first template to register the image to the set of capture spots; and
E) analyzing the image after the using D) in conjunction with spatial analyte data associated with each capture spot, thereby performing spatial analysis of analytes.