postProcessing package
Contents
postProcessing package¶
Submodules¶
postProcessing.mask_cellpose module¶
Created on Mon Jul 3 18:05:08 2023
@author: marcnol
Usage:
$ ls scan_*ROI.tif | mask_cellpose.py –gpu
or just for a single file
mask_cellpose.py –input scan_001_DAPI_001_ROI.tif –gpu
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postProcessing.mask_cellpose.find_label_in_path(mask_3d_path)¶
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postProcessing.mask_cellpose.find_roi_name_in_path(mask_3d_path)¶
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postProcessing.mask_cellpose.get_dict_shifts()¶
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postProcessing.mask_cellpose.load_json(file_name)¶ Load a JSON file like a python dict
- Parameters
file_name (str) – JSON file name
- Returns
Python dict
- Return type
dict
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postProcessing.mask_cellpose.load_params()¶
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postProcessing.mask_cellpose.main()¶
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postProcessing.mask_cellpose.parseArguments()¶
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postProcessing.mask_cellpose.process_images(cellprob=- 8, flow=10, stitch=0.1, diam=50, files=[], gpu=[False, None], cli=False, pretrained_model='cyto')¶
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postProcessing.mask_cellpose.run_cellpose(image_path, diam, cellprob, flow, stitch, folder_destination='segmentedObjects', gpu=[False, None], pretrained_model='cyto')¶
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postProcessing.mask_cellpose.run_cellpose_api(image_path, diam, cellprob, flow, stitch, gpu=[False, None], pretrained_model='cyto')¶
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postProcessing.mask_cellpose.shift_3d_mask(mask_3d_path)¶
postProcessing.mask_manual module¶
Created on Wed Oct 11 17:47:13 2023
@author: marcnol
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postProcessing.mask_manual.creates_user_mask(file_name, label)¶
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postProcessing.mask_manual.find_label_in_path(mask_3d_path)¶
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postProcessing.mask_manual.find_roi_name_in_path(mask_3d_path)¶
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postProcessing.mask_manual.get_dict_shifts()¶
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postProcessing.mask_manual.load_json(file_name)¶ Load a JSON file like a python dict
- Parameters
file_name (str) – JSON file name
- Returns
Python dict
- Return type
dict
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postProcessing.mask_manual.load_params()¶
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postProcessing.mask_manual.main()¶
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postProcessing.mask_manual.shift_3d_mask(mask_3d_path)¶
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postProcessing.mask_manual.show_image(data_2d, normalization='simple', size=(10, 10))¶
postProcessing.npy_to_tiff module¶
Created on Mon Mar 21 14:49:22 2022
@author: marcnol
converts NPY to TIFF
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postProcessing.npy_to_tiff.main()¶