New to CellProfiler but really enjoying it. I’m using it with worms, and the WormToolbox is running well.
I’ve been using the GUI v4.1.3 on macOS and it’s been working flawlessly. I am now working on implementing the headless version to run it at our high-throughput computing center.
For testing purposes, I created a simple pipeline that includes LoadData, ImageMath, and SaveImages. I created a temporary directory on my Desktop and adjusted the default output and input in the pipeline to
/Users/njwheeler/Desktop/temp_root/output/. In CreateBatchFiles, I set the local root path to
/Users/njwheeler/Desktop/temp_root/ and the cluster root path to
/. In LoadData, the module is directed to the Default Input Folder to find the CSV and the images. I’ve attached the CSV.
On the HTC, we will use Docker and I am testing the image on my local computer. I’ve attached the Docker file and conda_env.yml. The cellprofiler command works when I run it in the Docker image, but I can’t seem to load the actual images with the LoadData module. The command I run is
cellprofiler -c -r -p pipelines/Batch_data_minimal.h5 -L 10. I’ve attached the entirety of the error message.
At first I thought maybe my CSV was improperly formatted or I had an issue with the path translation between local/batch, and I suppose that still could be the case. However, in the log there is a line that says:
Getting image reader for: RawImage, None, file:/input/20210521-p01-KJG_A01.TIF. That image exists at that path, so it suggests that it’s finding the image but unable to read it.
RawImage is the image name (the header of the CSV is
Image_FileName_RawImage). I’m not sure what None refers to, perhaps that is part of my problem.
My Docker setup could be wrong, but I got the conda env directly from the CP GitHub.
I’m at a loss. Let me know if there is any missing information.