Spatially addressable molecular barcoding

A method for determining spatial locations of a plurality of targets in a sample, comprising:

• stochastically barcoding the plurality of targets in the sample using a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a pre-spatial label;
• concatenating one or more spatial label blocks onto the pre-spatial label to generate a spatial label;
• and
• identifying the spatial location of each of the plurality of targets using the spatial label.

A method for determining spatial locations of a plurality of targets in a sample, comprising:

• imaging the sample to generate a sample image;
• stochastically barcoding the plurality of targets in the sample using a plurality of stochastic barcodes to generate stochastically barcoded targets, wherein each of the plurality of stochastic barcodes comprises a spatial label;
• and
• identifying the spatial location of each of the plurality of targets using the spatial label.

A method for determining spatial locations of a plurality of singles cells, comprising:

• stochastically barcoding the plurality of singe cells using a plurality of synthetic particles,
• wherein each of the plurality of synthetic particles comprises a plurality of stochastic barcodes, a first group of optical labels, and a second group of optical labels,
• wherein each of the plurality of stochastic barcodes comprises a cellular label and a molecular label,
• wherein each optical label in the first group of optical labels comprises a first optical moiety and each optical label in the second group of optical labels comprises a second optical moiety, and
• wherein each of the plurality of synthetic particles is associated with an optical barcode comprising the first optical moiety and the second optical moiety;
• detecting the optical barcode of each of the plurality of synthetic particles to determine the location of each of the plurality of synthetic particles;
• and
• determining the spatial locations of the plurality of single cells based on the locations of the plurality of synthetic particles.

A method for identifying distinct cells in two or more samples, comprising:

• stochastically barcoding a plurality of targets in the two or more samples using a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label;
• estimating the number of the plurality of targets in the two or more samples using the molecular label;
• and
• distinguishing the two or more samples from each other using the spatial label, wherein the plurality of targets associated with stochastic barcodes with different spatial labels are from different samples.

A synthetic particle, comprising:

• a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a cellular label and a molecular label;
• a first group of optical labels;
• a second group of optical labels,
• wherein each optical label in the first group of optical labels comprises a first optical moiety and each optical label in the second group of optical labels comprises a second optical moiety, and
• wherein each of the plurality of synthetic particles is associated with an optical barcode comprising the first optical moiety and the second optical moiety.