When I used the -file-list flag I see images listed in the Images Module. We will use a CellProfiler example pipeline to analyse RNAi screening data from the Image Data Resource (IDR). Please correct any problems in your input module settings Now you are using the docker container as a shell. Peruse the documentation on the IdentifyPrimaryObjects module, for example, to get a sense of these, e.g., thresholding, declumping, and watershed. The pipeline cannot be started because of a configuration problem: The pipeline did not identify any image sets. The ExampleHuman.cppipe is a CellProfiler pipeline, the README is the usual README, and the images are the images that we want to analyze with the CellProfiler pipeline Earlier I said that your docker image is a computer. CellProfiler is capable of accurate and reliable segmentation of cells by utilizing a broad collection of classical image processing methods. $ cellprofiler -p segmentation.cppipe -data-file=exported_image_list_1.csv -r The pip freeze and java versions are given below. I then exported the pipeline file and copied it over to a Conda environment on a Ubuntu machine that has cellprofiler installed. It runs fine on a sample set of images and produces the desired output.
#CELLPROFILER PIPELINE MAC OS#
The error is "Encountered unrecoverable error in Images during startup: I created a pipeline using the CellProfiler 3.0.0 app on my Mac OS X. $ cellprofiler -p segmentation.cppipe -file-list=exported_image_list_1.csv -r I tried using both flags: -file-list and -data-file. When I run from the command line the GUI opens but images are not processed. However, I managed to reproduce the error with the new pipeline. PS - Im working on Ubuntu16.04 and installed cellprofiler using conda as described in the wiki. Please correct any problems in your input module settingsĪny suggestions or help would be appreciated The pipeline did not identify any image sets. The pipeline cannot be started because of The error that appears in the GUI after executing the command: $ cellprofiler -p IllumCorr/IC_pipeline_DAPI_GFAP_1.cppipe -data-file=exported_image_list.csv -rĮrror: CP-JAVA 00:07:15.006 WARN o.c.imageset.ChannelFilter - Empty image set list: no images passed the filtering criteria. I tried running the pipeline from the command line but didn't have much luck: Now I would like to process many more images and try to integrate with Python and command line. I exported the image list (exported_image_list.csv) and pipeline (IC_pipeline_DAPI_GFAP_1.cppipe). I'm trying to run a pipeline which I can successfully run using the GUI. First off thank you for the time and effort that goes into CellProfiler.
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