Summary

This was designed in trueSpace and printed on a Form1 at lowest resolution.

The center channel is constrained to 100 microns.
May be able to get down to 25-50 micron flow channel.
Will try to buff or grind optically clear side for particle counting.

An arduino UNO and a sparkfun light sensor (0.1 lux) might do the trick for a simple particle counter. Could use sheath fluid to narrow the center flow even more. Might even roughen the center lumen then stretch it on the Z-axis and twist to narrow the center. This might give an interesting vortex property to the channel flow.

Who knows, 3D printable Flow Cytometer?