Automated alignment of optics within a flow cytometer

A flow cytometer system comprising:

• a flow cell;
• a light source;
• a light path to direct light from said light source to said flow cell;
• an orientable mirror disposed in the light path that directs light from the light source into the flow cell;
• at least one detector that detects light from the flow cell;
• and
• a computer system with a control processor and programmed with computer program code executable by the processor to:
• starting with the mirror positioned at a first test orientation, control the mirror to change positioning of the mirror in a test orientation pattern from the first test orientation through a sequence of different test orientations of the mirror following the first test orientation;
• for each said test orientation of the mirror, control flowing of a validation fluid through the flow cell while the light source is operating to provide light to the mirror and collecting flow cytometry response data on light emitted from the flow cell with the mirror at the said test orientation, the validation fluid comprising a known concentration level of at least one known particle;
• analyze the flow cytometry response data to identify an alignment orientation for the mirror, comprising calculating from the flow cytometry response data for each test orientation of the mirror a concentration level of the at least one particle in the validation fluid and selecting the alignment orientation of the mirror based at least in part on the calculated concentration level of the at least one particle for each test orientation of the mirror;
• and
• control the mirror to be at a set orientation corresponding to the identified alignment orientation to align the mirror with the light source along the light path.