Python, conda, QuPath
.json or .json.zip: Pixelclassifiers that were trained in QuPath and saved as .json file. .json.zip can be unzipped to obtain .json.
For documentation on how to train pixel classifiers see here.
.groovy: Groovy script. Can be run in QuPath. For information on how to apply a groovy script on multiple images, see here.
.py: python files
environment.yml: contains conda environment under which .py files in this repository can run. Information from how to create an invironment from environment.yml can be found here.
Contains pixel-classifiers to segment tissue and CD11b+ cells in IHC slices of the pancreas
Contains files to segment exocrine and endocrine tissue
Contains .groovy files to randomly select a square tissue area within a bounding box. When applied to multiple images, all such-annotated regions can be combined into a composite image for training. (See here for instructions)
fine_grained_segmentation.groovy applies the pixel classifier endo_exo_bin_20240521.json to segment endocrine and exocrine tissue.
coarse_grained_segmentation.groovy simplifies the segments.
background.json allows to remove white background from the exocrine segment.
refine_exocrine.groovy segments edema within exocrine segments
export_edema_experimental.groovy generates mask images (png) of exocrine tissue and segmented edema
tile_image.py reads png images and generates non-overlapping tiles of them (saved as images in a specified output folder)
edema_to_graph_downsampled.py counts the number of branchpoints for each sample
For samples 14550 and 25868, tissue segmentation from the preveous edema segmentation were reused.
clearedema.groovy removes segmented edema
segment_necrosis.groovy loads the pixelclassifier necrosis_ignorebackground.json and segments necrosis.
mergenecrosis.groovy assignes pixels that are both classified as necrosis and endocrine to only endocrine
export_necrosis.groovy exports area-values of necrosis as a .csv file
exocrine11571.json was trained on samples of batch 11571. Exocrine tissue was segmented within the previous exocrine bounding box (excluding previous endocrine tissue).
new_exocrine.groovy subtracts white background segmented with background.json from exocrine segments.
necrosis2.json was trained on 11571 and applied to segment necrosis within the exocrine region (segment_necrosis.groovy).
export_necrosis.groovy exports areas-values of necrosis as a .csv file