A method of assaying single particles in a plurality of particles, said method comprising: capturing particles of said plurality in separate reaction volumes to produce a plurality of separate reaction volumes containing only one particle each such that the fraction of separate reaction volumes with only one particle each is at least 35% of the total number of separate reaction volumes; assaying a plurality of parameters for each particle(s) in each separate reaction volume, and wherein said assaying comprises: performing a plurality of reactions on each particle(s) in each separate reaction volume to produce a plurality of reaction products for each particle(s) in each separate reaction volume, wherein at least one reaction product is an amplicon produced by a reaction comprising nucleic acid amplification using at least two amplification primers, wherein each amplification primer comprises a barcode sequence; wherein the separate reaction volumes are separate compartments of a microfluidic device, the separate compartments being arranged as an array defined by rows and columns, wherein the combination of the first and second barcodes in each amplicon identifies the row and column of the compartment that was the source of the amplicon; recovering the contents of the separate reaction volumes by pooling reaction products from compartments in a row or in a column; and analyzing the reaction products to obtain results; disregarding results from any reaction volumes that contain no particles or contain more than a single particle; and associating remaining results of the assay with each separate reaction volume containing only one particle to produce a data set comprising a plurality of parameters for each particle in said plurality of particles that is in a separate reaction volume. capturing particles of said plurality in separate reaction volumes to produce a plurality of separate reaction volumes containing only one particle each such that the fraction of separate reaction volumes with only one particle each is at least 35% of the total number of separate reaction volumes; assaying a plurality of parameters for each particle(s) in each separate reaction volume, and wherein said assaying comprises: performing a plurality of reactions on each particle(s) in each separate reaction volume to produce a plurality of reaction products for each particle(s) in each separate reaction volume, wherein at least one reaction product is an amplicon produced by a reaction comprising nucleic acid amplification using at least two amplification primers, wherein each amplification primer comprises a barcode sequence; wherein the separate reaction volumes are separate compartments of a microfluidic device, the separate compartments being arranged as an array defined by rows and columns, wherein the combination of the first and second barcodes in each amplicon identifies the row and column of the compartment that was the source of the amplicon; recovering the contents of the separate reaction volumes by pooling reaction products from compartments in a row or in a column; and analyzing the reaction products to obtain results; performing a plurality of reactions on each particle(s) in each separate reaction volume to produce a plurality of reaction products for each particle(s) in each separate reaction volume, wherein at least one reaction product is an amplicon produced by a reaction comprising nucleic acid amplification using at least two amplification primers, wherein each amplification primer comprises a barcode sequence; wherein the separate reaction volumes are separate compartments of a microfluidic device, the separate compartments being arranged as an array defined by rows and columns, wherein the combination of the first and second barcodes in each amplicon identifies the row and column of the compartment that was the source of the amplicon; recovering the contents of the separate reaction volumes by pooling reaction products from compartments in a row or in a column; and analyzing the reaction products to obtain results; disregarding results from any reaction volumes that contain no particles or contain more than a single particle; and associating remaining results of the assay with each separate reaction volume containing only one particle to produce a data set comprising a plurality of parameters for each particle in said plurality of particles that is in a separate reaction volume.