I have just found your site, and sorry for not trying to dig further myself.
I read that it’s written in Python, but in the first tutorial I see the Matlab interface.
How does CellProfiler use Matlab?
Is it described in one of the tutorials?
Thanks for the inquiry! CellProfiler was programmed in Matlab originally, but ~4+ years ago it was rewritten into Python. So that tutorial must simply be quite old! (which one, btw?). So there is no direct Matlab interface for, say new image analysis algorithms, however that being said, the inputs and outputs often consist of CSV files (and images of course), which any number of analysis platforms can handle.
There are two templates for programming in python rather than matlab here: https://github.com/CellProfiler/CellProfiler/tree/master/cellprofiler/modules/plugins
Hope that helps!
Thank you very much for answering!
It’s a pity for me, because our group has decided that we switch to Matlab (from ImageJ+IgorPro), and I was very happy to find a Matlab program. I wonder how operational is the last Matlab release available on GitHub?
Is it a good idea to search there for the parts of Matlab code which would identify the cell membrane (labelled with a membrane dye)?
The tutorial that I first saw is the first one on the page
Accessible from the main page - Getting started - tutorials
Well, the last Matlab version will work I assume (it did then!). You can find it here: http://cellprofiler.org/previousReleases.html
and look under CellProfiler 1.0, where there is a link to the source code. I think it’s in Github too, though I’m not sure that the Matlab-> Python transition is tagged, so you’d have to search around 2009(!) on Github.
You can also search for other folks on the forum here who have posted about their Matlab solutions.