Methods and apparatus for full spectrum flow cytometer

A method for flow cytometry for a flow cytometer with a plurality of photodetectors, the method comprising:

• selecting a plurality of fluorochromes to label biological cells in a sample, wherein the number of the plurality of photodetectors in the flow cytometer is greater than the number of the selected plurality of fluorochromes;
• determining similarity indexes for each fluorochrome pair of the plurality of fluorochromes based on a configuration of the flow cytometer having a plurality of excitation lasers and the plurality of photodetectors, wherein each similarity index indicates a measure of fluorochrome interference between two spectra of fluorescence given off by each fluorochrome of each fluorochrome pair;
• generating a similarity matrix with the similarity indexes for each fluorochrome pair to visually display interaction between each fluorochrome pair;
• and
• displaying, on a display device to a user, the similarity matrix with each similarity index of each fluorochrome pair to evaluate the selection of the plurality of fluorochromes in the analysis of labeled biological cells in the sample.

A method for a spectral flow cytometer having N detector channels, the method comprising:

• running single stain reference controls for each of M fluorochromes through the flow cytometer to generate full spectrum signatures for each of the M fluorochromes being used to label particles/cells in a mixed sample, wherein M is less than N;
• forming an N by M reference matrix of reference vectors using the plurality of full spectrum signatures over the N detector channels;
• labeling the particles/cells in the mixed sample;
• running the labeled mixed sample through the flow cytometer to generate mixed signature data in a measured sample event vector for the labeled mixed sample;
• with the N by M reference matrix of reference vectors, unmixing the mixed signature data in the measured sample event vector to generate an unmixed sample event vector;
• and
• using the unmixed sample event vector to form one or more dot plots to display counts of the different types of particles/cells in the mixed sample to a user on a display device.