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annotation-hierarchy

Plugin implementation of structural hierarchy. Which structures should contain which other structures? Create inverse masks of tissue, excluding specific annotation layers. Define a new annotation based on characteristics of existing annotations.

autosegment-wsi

Playing around with zero-shot models for aiding annotation and quality control of segmentation outputs for whole slide images

cellkappavis

cluster_wsi_viewer

Simple visualization app built in Dash for Whole Slide Image clustering data

codex_featureextraction

Feature extraction plugin for registered CODEX and Histology Images

collagen_segmentation

deepcell-plugin

Plugin implementation of DeepCell for nucleus and cytoplasm segmentation in CODEX WSIs

digital_slide_archive

The official deployment of the Digital Slide Archive and HistomicsTK.

dn_classification

fusion

FUSION-Navigator visualization of spatially resolved molecular data in histology images.

fusion-annotation-model

Default segmentation model for use with the Annotation Station tool in FUSION

histo-cloud

histolab

Library for Digital Pathology Image Processing

interactive_nuclei_segmentation

Nuclei segmentation application to segment nuclei from patches in an image and write annotations to a text file

nuclei_segmentation_demo

Demonstration of nuclei segmentation in Matlab.

register-landmarks-plugin

Registering histology WSIs with high-resolution -omics image based on point landmarks.

spatialdata

An open and interoperable data framework for spatial omics data

squidpy-tutorials

Trying out some scverse for spatial data. Going through tutorials before contributing to figure out scanpy/anndata structures

write-ome-tif-plugin

Take an image on DSA and write it, with associated annotations, into ome-tif format. Include extra metadata in csv files if present.

wsi_annotations_kit

utility functions for generation, conversion, and saving annotation files for various whole slide image viewers

wsi_heatmap_viewer_app