TIA Centre Cytomine Apps

Cytomine apps developed by the TIA Centre, University of Warwick.

This repository contains three apps, all wrapping pre-trained models from TIAToolbox:

• cytomine-hovernet — nucleus instance segmentation and classification with HoVer-Net, trained on the PanNuke dataset.
• cytomine-kongnet — nucleus detection with KongNet, trained on the MONKEY Challenge dataset.
• cytomine-interactive-segmentation-nuclick — interactive nucleus segmentation from user-supplied click points with NuClick, trained on the PanNuke dataset.

See each app's README for model and reference details.

Pre-trained model weights

Weights are hosted on the TIA Centre HuggingFace:

• HoVer-Net (PanNuke): hovernet_fast-pannuke.pth
• KongNet (MONKEY): KongNet_MONKEY_1.pth
• NuClick (PanNuke): nuclick_light-pannuke.pth