Need help launching CellProfiler from command line


I’m pretty new to CellProfiler and Python. We would like to automate the CellProfiler. (either from command line or any available interfaces).
I’ve try following the instruction on the wiki (, some how, get this error:

[quote]C:\Projects\CellProfiler-master>python --help
Traceback (most recent call last):
File “”, line 14, in
import h5py
ImportError: No module named h5py[/quote]

Any help would be greatly appreciated.



We answered this offline, but for others, here was the response from our software engineer:

You probably want to install the current release of CellProfiler

I would strongly recommend running CellProfiler as a process rather than trying to use our code-base as a Python API. This page has some useful hints for running CellProfiler headless: … nvironment

Note that you can also create a list of images for analysis by CellProfiler. This is documented briefly on the LIMS page above and more extensively in the documentation for LoadData. We also integrate with OMERO (