Where did my cells go???
Cell loss happens mostly in the stage where cells are desiccated in the heater and injected into the plasma through the two cones called skimmer-reducer. But knowing that is not much comfort.
There are two workarounds for this issue. One is to inject a larger sample using the syringe pump (or other sample introduction method if you are feeling bold). Yet another is running several "repeats" of the sample and stitching together the resulting FCS files. Although I've never tried it myself the Broad Institute's GenePattern is supposed to have this feature.
What's your trick for getting more cell reads?