A method for recording cellular co-localization of RNA sequences and/or biomolecules tagged with an antibody conjugated to RNA in non-dissociated fixed cells or fixed tissue comprising (a) barcoding template nucleic acid sequences with unique molecular identifiers (UID's) before in situ amplification, wherein the template nucleic acid is cDNA, wherein the barcoding comprises adding at least one α-UID to each template nucleic acid by reverse transcription of said RNA, wherein at least one α-UID identifies targeted sequences or biomolecules of interest and wherein after extraction and amplification, all reads from the targeted sequence are identified as originating from a single template nucleic acid, wherein at least one α-UID may identify beacon sequences or biomolecules that are widely expressed, wherein a beacon sequence is a universally expressed gene, represented within the sample, and wherein after extraction and amplification, all reads from the beacon sequence or biomolecules are identified as originating from a single template sequence, wherein the α-UID is random or drawn from a pool of pre-defined nucleic acid sequences, thereby generating uniquely labeled target and optionally beacon nucleic acid sequences or biomolecules; (b) in situ amplification, by overlap extension PCR of the template nucleic acid sequences from (a), thereby labeling in situ association events of two or more uniquely labelled template amplification products during said in situ amplification with at least one β-UID, wherein the amplification is performed using homogenous heating of the entire sample or selective heating using directed infrared light sources to amplify only selected regions of interest, and wherein the amplification occurs in a hydrogel; wherein the β -UID is random, thereby generating uniquely labeled nucleic acid sequence-records of in situ association events; (c) isolation and amplification of the uniquely labeled products from (b), and (d) sequencing of the amplification products from (c) thereby recording cellular co-localization of RNA sequences and/or biomolecules tagged with an antibody conjugated to RNA in a non-dissociated fixed cell or fixed tissue. (a) barcoding template nucleic acid sequences with unique molecular identifiers (UID's) before in situ amplification, wherein the template nucleic acid is cDNA, wherein the barcoding comprises adding at least one α-UID to each template nucleic acid by reverse transcription of said RNA, wherein at least one α-UID identifies targeted sequences or biomolecules of interest and wherein after extraction and amplification, all reads from the targeted sequence are identified as originating from a single template nucleic acid, wherein at least one α-UID may identify beacon sequences or biomolecules that are widely expressed, wherein a beacon sequence is a universally expressed gene, represented within the sample, and wherein after extraction and amplification, all reads from the beacon sequence or biomolecules are identified as originating from a single template sequence, wherein the α-UID is random or drawn from a pool of pre-defined nucleic acid sequences, thereby generating uniquely labeled target and optionally beacon nucleic acid sequences or biomolecules; wherein the barcoding comprises adding at least one α-UID to each template nucleic acid by reverse transcription of said RNA, wherein at least one α-UID identifies targeted sequences or biomolecules of interest and wherein after extraction and amplification, all reads from the targeted sequence are identified as originating from a single template nucleic acid, wherein at least one α-UID may identify beacon sequences or biomolecules that are widely expressed, wherein a beacon sequence is a universally expressed gene, represented within the sample, and wherein after extraction and amplification, all reads from the beacon sequence or biomolecules are identified as originating from a single template sequence, wherein the α-UID is random or drawn from a pool of pre-defined nucleic acid sequences, thereby generating uniquely labeled target and optionally beacon nucleic acid sequences or biomolecules; (b) in situ amplification, by overlap extension PCR of the template nucleic acid sequences from (a), thereby labeling in situ association events of two or more uniquely labelled template amplification products during said in situ amplification with at least one β-UID, wherein the amplification is performed using homogenous heating of the entire sample or selective heating using directed infrared light sources to amplify only selected regions of interest, and wherein the amplification occurs in a hydrogel; wherein the β -UID is random, thereby generating uniquely labeled nucleic acid sequence-records of in situ association events; (c) isolation and amplification of the uniquely labeled products from (b), and (d) sequencing of the amplification products from (c) thereby recording cellular co-localization of RNA sequences and/or biomolecules tagged with an antibody conjugated to RNA in a non-dissociated fixed cell or fixed tissue.