Automated alignment of optics within a flow cytometer

1. 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.

2. A system according to claim 1 , wherein:

the mirror has a reflective surface and a central axis extending perpendicular to the reflective surface, and at each said test orientation of the mirror, the central axis intersects a plane transverse to the light path between the mirror and the flow cell at a separate intersection location on the plane; and

the sequence of different orientations of the mirror results in the intersection locations being in a uniformly spaced grid on the plane.

3. A system according to claim 2 , wherein the uniformly spaced grid is centered around a first intersection location associated with the first test orientation of the mirror.

4. A system according to claim 3 , wherein the uniformly spaced grid is traversed in a fixed pattern starting from the first intersection location.

5. A system according to claim 4 , wherein the fixed pattern minimizes reversals of the direction in which one or more motors coupled to the mirror are operated to change the orientation of the mirror from the first test orientation to each of the different test orientations of the mirror.

6. A system according to claim 4 , wherein the fixed pattern comprises one of a clockwise and a counter-clockwise pattern spiraling outward from the first intersection location.

7. A system according to claim 4 , further comprising:

one or more motors coupled to the orientable mirror, wherein said one or more motors are in communication with said processor and the computer system is programmed with the computer program code executable by the processor to return the mirror to the first test orientation of the mirror and to change the orientation of the mirror from the first test orientation to each of the different test orientations of the mirror.

8. A system according to claim 7 , wherein said computer system is programmed with the computer program code executable by the processor to conduct a motor mapping procedure to obtain a current absolute mirror orientation.

9. A system according to claim 8 , wherein the motor mapping procedure is conducted prior to operating said one or more motors coupled to the orientable mirror to return the mirror to the first test orientation.

10. A system according to claim 8 , wherein each of said one or more motors comprises a linear stepper motor to drive linear motion steps, and wherein said computer system is programmed with the computer program code executable by the processor to conduct the motor mapping procedure by:

operating each of said one or more motors until each motor has reached a minimum linear position limit of the motor;

operating each of said one or more motors until each motor has reached a maximum linear position limit of the motor; and

counting the number of linear motion steps of each of said one or more motors between the minimum linear motion limit and the maximum linear motion limit of the motor.

11. A system according to claim 10 , wherein each said linear motion step of each of said one or more motors corresponds to no more than 300 nanometers of linear motion.

12. A system according to claim 7 , wherein said computer system is programmed with the computer program code executable by the processor to apply a motor backlash parameter associated with each of said one or more motors when said each of said one or more motors reverses direction.

13. A system according to claim 1 , wherein said computer system is programmed with the computer program code executable by the processor to analyze the flow cytometry response data to identify the alignment orientation of the mirror by:

for each test orientation of the mirror, calculating one or more additional metrics from the flow cytometry response data in addition to the calculated concentration level of the at least one particle;

normalizing and weighting the calculated concentration levels and the additional metrics; and

listing each test orientation of the mirror in order of response quality based on the normalized and weighted calculated concentration levels and the additional metrics.

14. A system according to claim 13 , wherein the additional metrics include an average signal peak height of the time series signal data trace corresponding with each test orientation of the mirror.

15. A system according to claim 1 , wherein the mirror is rotatable around two axes of rotation to achieve each test orientation of the mirror.

16. A system according to claim 15 , wherein:

a first one of the two axes of rotation comprises a tip axis of the mirror correlated with positioning of the light from the light source and reflected from the mirror in a first direction relative to the flow cell; and

a second one of the two axes of rotation comprises a tilt axis of the mirror correlated with positioning of the light from the light source and reflected from the mirror in a second direction relative to the flow cell.

17. A system according to claim 16 wherein the first direction comprises a vertical direction and the second direction comprises a horizontal direction.

18. A system according to claim 1 , wherein said computer system is programmed with the computer program code executable by the processor to:

reset the first test orientation of the mirror to coincide with the alignment orientation of the mirror.