A method for determining the presence and/or abundance of an immune cell clonotype at a location in a tissue section, the method comprising: (a) contacting the tissue section with an array comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises (i) a primer binding site, (ii) a spatial barcode and (iii) a capture domain that binds to a poly(A) sequence of a nucleic acid encoding an immune cell receptor of the immune cell clonotype; (b) extending a 3' end of the capture probe using the nucleic acid encoding the immune cell receptor as a template, thereby generating an extended capture probe; generating a second strand of nucleic acid that comprises (i) a sequence that is complementary to all or a portion of the primer binding site, (ii) a sequence that is complementary to all or a portion of the spatial barcode, and (iii) a sequence that corresponds to all or a portion of the sequence of the nucleic acid encoding the immune cell receptor; enriching the obtained nucleic acid encoding the immune cell receptor of the immune cell clonotype, wherein enriching comprises hybridizing a plurality of hybridization probes to the obtained nucleic acid encoding the immune cell receptor of the immune cell clonotype, wherein a hybridization probe comprises (i) a sequence complementary to a portion of the nucleic acid encoding the immune cell receptor and (ii) a binding moiety that interacts with a capture moiety; and determining (i) all or a portion of the sequence of the spatial barcode or a complement thereof, and (ii) all or a portion of the sequence of the nucleic acid encoding the immune cell receptor or a complement thereof, and using the determined sequences of (i) and (ii) to determine the presence and/or abundance of the immune cell clonotype at the location in the tissue section. (a) contacting the tissue section with an array comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises (i) a primer binding site, (ii) a spatial barcode and (iii) a capture domain that binds to a poly(A) sequence of a nucleic acid encoding an immune cell receptor of the immune cell clonotype; (b) extending a 3' end of the capture probe using the nucleic acid encoding the immune cell receptor as a template, thereby generating an extended capture probe; generating a second strand of nucleic acid that comprises (i) a sequence that is complementary to all or a portion of the primer binding site, (ii) a sequence that is complementary to all or a portion of the spatial barcode, and (iii) a sequence that corresponds to all or a portion of the sequence of the nucleic acid encoding the immune cell receptor; enriching the obtained nucleic acid encoding the immune cell receptor of the immune cell clonotype, wherein enriching comprises hybridizing a plurality of hybridization probes to the obtained nucleic acid encoding the immune cell receptor of the immune cell clonotype, wherein a hybridization probe comprises (i) a sequence complementary to a portion of the nucleic acid encoding the immune cell receptor and (ii) a binding moiety that interacts with a capture moiety; and determining (i) all or a portion of the sequence of the spatial barcode or a complement thereof, and (ii) all or a portion of the sequence of the nucleic acid encoding the immune cell receptor or a complement thereof, and using the determined sequences of (i) and (ii) to determine the presence and/or abundance of the immune cell clonotype at the location in the tissue section. <EOS>