VollSeg & KapoorLabs Tools — Tutorials for 3D Cell Segmentation, Tracking and Object Detection
A collection of tutorials for the KapoorLabs suite of open-source bioimage analysis tools. VollSeg brings deep-learning based 3D cell segmentation into napari and TrackMate, combining detection, instance segmentation and tracking of cells in challenging 3D microscopy data.
Topics covered:
- VollSeg 2D and 3D segmentation workflows in napari (slice-by-slice labelling, 3D labelling, the Big Stitcher viewer)
- Tracking cells in 3D with TrackMate, using the biology and physics of cell motion (LAP and SimpleLAP trackers, RANSAC filtering on MultiKymograph-generated kymographs)
- Oneat — event-based network extensions for TrackMate to correct tracks and verify lineage trees
- Hands-on object detection tutorials with a minimalist YOLO implementation, including playing with YOLO loss terms
- Community demos and I2K (Images to Knowledge) full tutorials
All tools are open source and available as napari plugins and Fiji/TrackMate extensions from KapoorLabs.
