I have a pipeline that perform illumination correction and segmentation. Similar to the one the “advance segmentation” from the tutorial Headless CellProfiler/ DistributedCellProfiler Tutorial.
I have a load_data_with_illum.csv that contains the necessary info to load the .tiff images, and the .npy (calculated beforehand).
When I run the pipeline headless in my machine, It works. However, when I tried to run it in the cloud (GCP), using pretty much the same headless command, It doesn’t work. And I keep getting the following error:
Error detected during run of module CorrectIlluminationApply
Traceback (most recent call last):
File “/usr/local/lib/python3.8/dist-packages/cellprofiler_core/pipeline/_pipeline.py”, line 958, in run_with_yield
File “/usr/local/lib/python3.8/dist-packages/cellprofiler_core/pipeline/_pipeline.py”, line 1275, in run_module
File “/usr/local/lib/python3.8/dist-packages/cellprofiler/modules/correctilluminationapply.py”, line 233, in run
File “/usr/local/lib/python3.8/dist-packages/cellprofiler/modules/correctilluminationapply.py”, line 249, in run_image
illum_function = workspace.image_set.get_image(illum_correct_name)
File “/usr/local/lib/python3.8/dist-packages/cellprofiler_core/measurement/_measurements.py”, line 1534, in get_image
ValueError: The IllumER image is missing from the pipeline.
- I’ve verified and re-verified that the .npy files were there, and the path in the load_csv_will_illum.csv were the correct ones, But still it doesn’t find those images.
-If I uncheck the illumination correction from the pipeline, save it, and upload it, the pipeline run without any issue. Meaning that it can find the tiff images. But for some reason it can not find the .npy
Thank you in advance,