I want to run my pipeline on thousands of images.
The images are stored in hundreds of folder like
I made my pipeline to produce for each folder,
- store resultant overlayImages on /home/myID/Desktop/Output/Patient_A
- store data spreadsheets on /home/myID/Desktop/Output/Patient_A/Data
I want to run the pipeline headless on /home/myID/Desktop/Input, so that the pipeline runs on hundreds of folders in the folder. but i don’t know what to do with .the batch command
/python-2.6.sh CellProfiler.py -p <Default_Output_Folder_path>/Batch_data.h5 -c -r -b -f <first_image_set_number> -l <last_image_set_number>
…any kind of help would be greatly appreciated. Thanks!