Alignment beads for mfish

A kit, comprising:

• a plurality of targeting probe sets, each targeting probe set of the plurality of targeting probe set including a multiplicity of targeting probes, each targeting probe of the multiplicity of targeting probes configured to bind to the same analyte in a sample, and targeting probes of different sets configured to bind to different analytes;
• a plurality of fiducial markers, wherein each fiducial marker comprises a plurality of binding site sets, each binding site set of the plurality of binding site sets including a multiplicity of binding sites;
• a plurality of readout probe sets, each readout probe set of the plurality of readout probe sets including a multiplicity of readout probes, each readout probe of a particular readout probe set configured to bind to binding sites of a particular set of binding sites from the plurality of binding site sets and to bind to targeting probes of a particular set of targeting probes from the plurality of binding probe sets, each readout probe including a fluorescent moiety.