HistoJS
HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images - Published in JOSS (2024)
tiatoolbox
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
yeast-in-microstructures-dataset
Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].
tyc-dataset
Official and maintained implementation of the dataset paper "The TYC Dataset for Understanding Instance-Level Semantics and Motions of Cells in Microstructures" [ICCVW 2023].
cell-detr
Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].
https://github.com/bmcv/superdsm
SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.
spatialvpt
Segmentation and QC workflow for MERSCOPE using vizgen-postprocessing tool
https://github.com/chenliu-1996/diffkillr
[ICASSP 2025 Oral] DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images