Integration with Matlab (import/export data)

Hello,

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!
Kirill

Hi Kirill,

There is no specific bridge for importing/exporting MATLAB data to and from CellProfiler; the version of CellProfiler makes no difference, unfortunately.

What I suggest is using a MATLAB script to create your image matrices, and then have it call CellProfiler in “headless” mode, i.e, without the UI, and feed it the pipeline and the input images. Then, once the CellProfiler analysis is done, your script can read in the CellProfiler output and continue. You can find more information on running CellProfiler headless by going to Help > Other Features > Batch Processing, or more specifically, running ‘cellprofiler --help’ from the command line for a listing of the input arguments you can use.

Regards,
-Mark