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slideQuantify_v2_README.txt
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slideQuantify_v2_README.txt
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Instructions for SlideQuantify_V2
Call the script like:
bash slideQuantify_V2 [arg1: STAIN] [arg2: path_to_cellprofiler_pipeline] [arg3: path_to_working_directory] [arg4: path_to_procces_file] [arg5: y.name@umcutrecht.nl] [arg6: FAIL] [arg7: 2000] [arg8: 2] [args9: path/to/dir (OPTIONAL)]"
e.g:
bash slideQuantify_V2 EVG ./EVG.cp413.v1.1.cppipe ./ ./all_snr.txt t.s.peters-4@umcutrecht.nl NONE 2000 1 ./masks/
or
bash slideQuantify_V2 EVG ./EVG.cp413.v1.1.cppipe ./ ./all_snr.txt t.s.peters-4@umcutrecht.nl NONE 2000 1
Things to note:
- arg3: path_to_working_directory:
This directory should contain the folders _ndpi and/or _tif containing the images to process.
e.g:
- _ndpi
- AE1....
- AE2....
- ....
- _tif
- AE3....
- AE4....
- ....
- arg4: path_to_procces_file:
This should be a .txt file containing a list of all study numbers to process.
e.g:
study_numbers.txt
AE1
AE2
AE3
AE4
....
- arg9:
This is an optinal parameter. If used it should point to a directory containing the masks for the images you want to process.
If left empty, masks will be created using EntropyMasker