CellProfiler 1.0 -> 2.0 module conversions?


I am a new CP user and I am interested in using the modules from “Image-based transcriptomics in thousands of single human cells at single-molecule resolution” Nico Battich, Thomas Stoeger & Lucas Pelkmans Nature Methods 10, 1127–1133 (2013), http://dx.doi.org/10.1038/nmeth.2657, available here: http://www.nature.com/nmeth/journal/v10/n11/extref/nmeth.2657-S6.zip. The posted files are .m, so I expect these need to be converted to .py. Is this correct? If so, any chance these have been converted for CP2.0?

If not, is it correct that CP1.0 modules can be saved into CP1.0 pipelines and then loaded in CP2.0. I tried to install CP1.0 (9717) to try this, but got an error about a missing mclmcrrt710.dll. I chased this down to a r2009a 7.10, but this appears to be no longer available for download from MATLAB. If this is correct, is there another way to get a version of MATLAB with this dll so that I can put together a CP1.0 pipeline for use in CP2.0?

Thank you,


Hi Jason,

You are correct in that these .m files would need to be converted to .py files. However, to our knowledge, this has not been done for these plugins (i.e, user-written modules outside of the ones that are bundled with CellProfiler). Also, while CP 1.0 modules are indeed converted for CP 2.0 (and now for CP 2.1), this is not the case for plugins that others have written. You might want to contact the paper authors and see if they might have done the conversion themselves.

Also, re installing CP 1.0: Did you install the MATLAB Compiler Runtime (MCR) that goes along with v9717? If not, it should be available from the download page for prior versions: cellprofiler.org/previousReleases.shtml