This software implements the pipeline for the lymphocyte classification project.

List of folders and functionalities are below:

scripts/: contains scripts that connect several sub-functionalities together for complete functionalities such as generating camicroscope heatmaps given svs images.

conf/: contains configuration.

csv_generation/: generates csv files which are the input of the clustering algorithm.

data/: a place where should contain all logs, input/output images, trained CNN models, and large files.

download_heatmap/: downloads grayscale lymphocyte or tumor heatmaps, and thresholds grayscale heatmaps to binary heatmaps.

heatmap_gen/: generate json files that represents heatmaps for camicroscope, using the lymphocyte and necrosis CNNs' raw output txt files.

patch_extraction/: extracts all patches from svs images. Mainly used in the test phase.

patch_extraction_from_list/: extracts patches from a list. Used in scenarios like extracting training patches, and extracting stratified sampled patches for rethresholding purpose.

patch_labeling_web/: a website that label each image as positive/negative/ignore.

patch_sampling/: samples patches in a stratified manner. Input: grayscale heaetmaps. Output: a list of patches for patch_extraction_from_list/ to extract.

prediction/: CNN prediction code.

training/: CNN training code.

third_party/: third party code for CNN.