A method for identifying location and/or abundance of an analyte in a biological sample, the method comprising: (a) recording a cellular activity and/or an intracellular gene expression of a nucleic acid of the biological sample, wherein the biological sample is located within a perfusion chamber of a plurality of perfusion chambers, wherein the perfusion chamber comprises a substrate and a gasket; (b) contacting the biological sample with the substrate comprising a plurality of capture probes, wherein a capture probe of the plurality of the capture probes comprises (i) a spatial barcode and (ii) a capture domain that binds specifically to a sequence present in the analyte; (c) extending the capture probe using the analyte that is specifically bound to the capture domain as a template, thereby generating an extended capture probe; (d) amplifying the extended capture probe to produce a plurality of extended capture probes; and (e) determining (i) all of the sequence of the spatial barcode, or a complement thereof, and (ii) all or part of the sequence of the analyte, or a complement thereof, and using the determined sequences of (i) and (ii) to identify the location and/or the abundance of the analyte in the biological sample; wherein the method further comprises: mounting the gasket onto the substrate, wherein the substrate comprises a plurality of substrate regions, wherein a substrate region of the plurality of substrate regions comprises the capture probe comprising (i) the spatial barcode and (ii) the capture domain that binds specifically to the sequence present in the analyte, wherein the gasket comprises (i) a plurality of apertures corresponding to the plurality of substrate regions, respectively, (ii) a plurality of input channels being fluidly connected to the plurality of apertures, respectively, and (iii) a plurality of output channels being fluidly connected to the plurality of apertures, respectively, and wherein the plurality of apertures of the gasket are aligned with the plurality of substrate regions of the substrate when the gasket is mounted onto the substrate; and mounting a cover onto the gasket to define a plurality of perfusion chambers, wherein the cover includes an inlet and an outlet, the inlet being fluidly connected to the plurality of input channels when the cover is mounted onto the gasket, the outlet being fluidly connected to the plurality of output channels when the cover is mounted onto the gasket, and wherein the plurality of perfusion chambers are defined by (i) the plurality of substrate regions of the substrate, (ii) the plurality of apertures of the gasket that is mounted onto the substrate, and (iii) the cover that is mounted onto the gasket. (a) recording a cellular activity and/or an intracellular gene expression of a nucleic acid of the biological sample, wherein the biological sample is located within a perfusion chamber of a plurality of perfusion chambers, wherein the perfusion chamber comprises a substrate and a gasket; (b) contacting the biological sample with the substrate comprising a plurality of capture probes, wherein a capture probe of the plurality of the capture probes comprises (i) a spatial barcode and (ii) a capture domain that binds specifically to a sequence present in the analyte; (c) extending the capture probe using the analyte that is specifically bound to the capture domain as a template, thereby generating an extended capture probe; (d) amplifying the extended capture probe to produce a plurality of extended capture probes; and (e) determining (i) all of the sequence of the spatial barcode, or a complement thereof, and (ii) all or part of the sequence of the analyte, or a complement thereof, and using the determined sequences of (i) and (ii) to identify the location and/or the abundance of the analyte in the biological sample; wherein the substrate comprises a plurality of substrate regions, wherein a substrate region of the plurality of substrate regions comprises the capture probe comprising (i) the spatial barcode and (ii) the capture domain that binds specifically to the sequence present in the analyte, wherein the gasket comprises (i) a plurality of apertures corresponding to the plurality of substrate regions, respectively, (ii) a plurality of input channels being fluidly connected to the plurality of apertures, respectively, and (iii) a plurality of output channels being fluidly connected to the plurality of apertures, respectively, and wherein the plurality of apertures of the gasket are aligned with the plurality of substrate regions of the substrate when the gasket is mounted onto the substrate; and mounting a cover onto the gasket to define a plurality of perfusion chambers, wherein the cover includes an inlet and an outlet, the inlet being fluidly connected to the plurality of input channels when the cover is mounted onto the gasket, the outlet being fluidly connected to the plurality of output channels when the cover is mounted onto the gasket, and wherein the plurality of perfusion chambers are defined by (i) the plurality of substrate regions of the substrate, (ii) the plurality of apertures of the gasket that is mounted onto the substrate, and (iii) the cover that is mounted onto the gasket.