I’m very new to Cell Profiler, so I apologize if my question is too simple, or has been addressed previously (though I took a look at the FAQ and did a quick forum search).
I was wondering, whether there is a comprehensible guide for integrating Matlab with Cell Profiler. For instance, I would like to have an Matlab script that would first run a certain image processing algorithm in Matlab (say, a third-party canny edge detection), then export the resulting multidimensional image matrix as a pipeline into Cell Profiler for object recognition/analysis, then export the result back into Matlab for additional processing and analysis. Can I accomplish that? The cp2.1.0_manual_0c7fb94.pdf manual doesn’t seem to address that subject. I also looked at the “ExampleInSituSequencing” matlab files, but the InSituSeq_decoding.m code is a bit hard to follow.
Also, should I be even using the Cell Profiler 2.1 for that purpose? Would the CellProfiler Analyst 2.0 or the CellProfiler 1.0 version better serve me?
Thank you in advance!