A method for detecting a plurality of analytes in a cell or tissue sample, comprising: (a) mounting the cell or tissue sample on a solid support; (b) contacting the cell or tissue sample with a composition comprising a plurality of detection reagents, the plurality of detection reagents comprising a plurality of subpopulations of detection reagents; (c) incubating the cell or tissue sample together with the plurality of detection reagents for a sufficient amount of time to allow binding of the plurality of detection reagents to the analytes; wherein each subpopulation of the plurality of detection reagents targets a different analyte, wherein each of the plurality of detection reagents comprises: a probe reagent targeting an analyte of the plurality of analytes and one or a plurality of pre-determined subsequences, wherein the probe reagent and the one or the plurality of pre-determined subsequences are conjugated together; (d) detecting in a temporally-sequential manner the one or the plurality of pre-determined subsequences, wherein the detecting comprises: (i) hybridizing a set of decoder probes with a subsequence of the detection reagents, wherein the set of decoder probes comprises a plurality of subpopulations of decoder probes and wherein each subpopulation of the decoder probes comprises a detectable label, each detectable label producing a signal signature; (ii) detecting the signal signature produced by the hybridization of the set of decoder probes; (iii) removing the signal signature; and (iv) repeating (i) and (iii) using a different set of decoder probes to detect other subsequences of the detection reagents, thereby producing a temporal order of the signal signatures unique for each subpopulation of the plurality of detection reagents; and (e) using the temporal order of the signal signatures corresponding to the one or the plurality of the pre-determined subsequences of the detection reagent to identify a subpopulation of the detection reagents, thereby detecting the plurality of analytes in the cell or tissue sample. (a) mounting the cell or tissue sample on a solid support; (b) contacting the cell or tissue sample with a composition comprising a plurality of detection reagents, the plurality of detection reagents comprising a plurality of subpopulations of detection reagents; (c) incubating the cell or tissue sample together with the plurality of detection reagents for a sufficient amount of time to allow binding of the plurality of detection reagents to the analytes; wherein each subpopulation of the plurality of detection reagents targets a different analyte, wherein each of the plurality of detection reagents comprises: a probe reagent targeting an analyte of the plurality of analytes and one or a plurality of pre-determined subsequences, wherein the probe reagent and the one or the plurality of pre-determined subsequences are conjugated together; (d) detecting in a temporally-sequential manner the one or the plurality of pre-determined subsequences, wherein the detecting comprises: (i) hybridizing a set of decoder probes with a subsequence of the detection reagents, wherein the set of decoder probes comprises a plurality of subpopulations of decoder probes and wherein each subpopulation of the decoder probes comprises a detectable label, each detectable label producing a signal signature; (ii) detecting the signal signature produced by the hybridization of the set of decoder probes; (iii) removing the signal signature; and (iv) repeating (i) and (iii) using a different set of decoder probes to detect other subsequences of the detection reagents, thereby producing a temporal order of the signal signatures unique for each subpopulation of the plurality of detection reagents; and (i) hybridizing a set of decoder probes with a subsequence of the detection reagents, wherein the set of decoder probes comprises a plurality of subpopulations of decoder probes and wherein each subpopulation of the decoder probes comprises a detectable label, each detectable label producing a signal signature; (ii) detecting the signal signature produced by the hybridization of the set of decoder probes; (iii) removing the signal signature; and (iv) repeating (i) and (iii) using a different set of decoder probes to detect other subsequences of the detection reagents, thereby producing a temporal order of the signal signatures unique for each subpopulation of the plurality of detection reagents; and (e) using the temporal order of the signal signatures corresponding to the one or the plurality of the pre-determined subsequences of the detection reagent to identify a subpopulation of the detection reagents, thereby detecting the plurality of analytes in the cell or tissue sample.