Loads the cellprofiler container module and runs the CellProfiler.py script inside the container, and This scriptĭefines a job array with 100 tasks, each task processing a single image, Create/edit Slurm job script /scratch/mstk/cp_jobs/cellprofiler.slurm (see below).The following two steps create the Slurm job script and submit it to the cluster: Let us assume that we have a directory with 100 image files to process in /scratch/$USER/images and that we completed steps 1-3 as described above. The easiest way to implement parallel image processing with CellProfiler is to create a job array where each job in the array (referred to as job array task) processes a unique subset of the total image set. Create and submit the Slurm job scriptĪ general premise in the batch processing workflow is that processing of images can occur independently from each other in a parallel fashion. So steps 2 and 3 need to be repeated when you want to process images in a different directory. Note: The pipeline batch file created in step 3 contains hardcoded paths to the to-be-processed image files. This will create the file Batch_data.h5 which defines the entire image processing step including paths to the images.
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