![]() How can I specify the input image set? Can I do it using the Python package? Hi for the swift response! A few follow-up questions: If there was some method (whether in beta development or not) of running a CellProfiler pipeline from a Python script without running into this error, I would love to know about it. Here is a GitHub issue that seems to express the exact same problem (albeit with CellProfiler v3.1.8): However, if I run the pipeline in the command line headless mode, it works fine. ![]() Ldr = static_call('java/lang/ClassLoader', 'getSystemClassLoader',įile "/home/jupyter-user/miniconda/envs/preprocessing/lib/python3.8/site-packages/javabridge/jutil.py", line 939, in static_callįn = make_static_call(class_name, method_name, sig)įile "/home/jupyter-user/miniconda/envs/preprocessing/lib/python3.8/site-packages/javabridge/jutil.py", line 910, in make_static_callĪttributeError: 'NoneType' object has no attribute 'find_class' ![]() Ifcls = javabridge.class_for_name("")įile "/home/jupyter-user/miniconda/envs/preprocessing/lib/python3.8/site-packages/javabridge/jutil.py", line 1743, in class_for_name Unfortunately, this gives me the following Javabridge error: Traceback (most recent call last):įile "/home/jupyter-user/miniconda/envs/preprocessing/lib/python3.8/site-packages/cellprofiler_core/pipeline/_pipeline.py", line 1402, in prepare_runįile "/home/jupyter-user/miniconda/envs/preprocessing/lib/python3.8/site-packages/cellprofiler_core/modules/images.py", line 335, in prepare_run I followed the guide at below is the script: from cellprofiler_core.pipeline import Pipeline Then, I tried to run the pipeline using CellProfiler as a Python package. Somehow, I got this all working, and I’m even able to open the CellProfiler GUI via the Linux Docker container that my MacBook Pro is running (although there were a few bugs with the installation that I had to manually patch I’m happy to share those if anyone is interested).įor the next step, I created a CellProfiler cell segmentation pipeline using the GUI, and then I exported it as a. Therefore, I decided to download the latest CellProfiler code from GitHub, apt-get all of the various dependencies, build CellProfiler “from source”, and package it all as a Docker container. So to preface this post, I realize that CellProfiler 4.0.0 is still under development, but I desperately need to use Python 3 with CellProfiler for a software package that I am developing. ![]()
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