Having Trouble Getting Started!

I’m interested in using CellProfiler to measure the transport rates of particles moving along axons. These particles frequently move under/over one another, which has so far confounded all automated tracking techniques. I’ve been generating kymographs of the these axons and measuring the particle movement rates, stall durations, and reversals manually, but this is slow and tedious.

I downloaded the example pipeline for sorting what looks like mitotic cells, but it didn’t seem to work well for my movies. What’s a good way to get started on this, remembering that the particles I"m interested in principally move along a single axis? I can submit example movies/images if needed.

Thanks for your help!


You can first take a look at our example tracking pipeline here: cellprofiler.org/examples.shtml#Tracking

But note that particles moving over/under or seeming to split and merge are quite hard to deconvolve, especially if the directions can reverse. One would need a motion model that includes reversals and (to my knowledge, as of yet) ours doesn’t. Even with the module TrackObjects->LAP method, there are two motions models assumed: either static or moving in one direction.

But give the TrackObjects->LAP method a try! It is not easy to configure, but feel free to post your pipeline attempt and we might be able to help further.