CellProfiler 2.1.1 not writing output file?

I have compiled CellProfiler 2.1.1 for Linux, and it seems to work when I run a pipeline
with the (deprecated) LoadImages module. I run headless from the command line. What’s
not working is the creation of the matlab output files. I went to the output settings, and
selected “Write Matlab file” with an output folder. But no mat-file is created after the full
analysis. The Export module (exporting to CSV) works and the folder is created. Am I doing
something wrong?

On a side note, is it correct that “Write Matlab file” is a CellProfiler configuration setting,
and not a pipeline or command-line setting? That would be quite unfortunate, because I run
multiple headless CellProfiler concurrently, and sometimes I need Matlab files, sometimes

Thanks for your help!

CellProfiler 2.1.x writes its measurements to an HDF5 file and, at the end of analysis in UI mode, copies the measurements from the HDF5 file to a matlab file if that’s what you’ve asked for. I’m not sure if I have a test for this though and we use it so infrequently that it’s possible that something is broken.

In headless mode, CellProfiler should be figuring out whether you want a Matlab file by the extension you give for the measurement file. So we are committed to making that work too.

I’ll put looking into this on my to-do list and give you a more thorough answer about what works for me.

Hi Mario,
Here are the details:

The first argument on the CellProfiler command-line, other than switches, is the path name of the measurements file to be saved. If the file name ends in “.mat” (case-sensitive), the measurements are copied from a temporary HDF5 file to a matlab file with that path name, otherwise the file name is used as the HDF5 measurements file name and measurements are saved incrementally during the course of the run. If there’s no path, the file is saved to the current directory - you might expect that it would be saved to the output directory, but it’s not.

Here’s the command line that I used:

Hi Lee,
thanks for the reply, this makes sense! I will test that it works and report back!
Cheers, Mario