Tools & remarks

Convenient tools

• Generic tools
  • Napari: interactive multidimensional image viewer and annotation tool, with a rich plugin ecosystem
• Segmentation tools (ML based)
  • StarDist: robust nucleus and cell instance segmentation using star-convex shapes
  • Cellpose: generalist deep-learning segmentation for many cell types
  • micro-sam: SAM-based interactive and automated segmentation workflows for microscopy
  • OrganoidTracker: tracking and lineage analysis for organoid time-lapse data
  • ilastik: pixel/object classification and segmentation with minimal coding
  • biapy: (generic) deep learning-based segmentation and tracking for bioimage analysis

Additional tools (suggested by LLM):

• SimpleITK: medical/microscopy image analysis tool package
• Squidpy: spatial omics analysis with image feature extraction support

Convenient non-python tools:

• Fiji/ImageJ: classic GUI platform with many plugins and macro support
  • Labkit: interactive machine learning segmentation in Fiji
  • TrackMate: particle/cell tracking in Fiji
• CellProfiler: pipeline-based high-throughput image analysis and feature extraction

An extensive list of bio-image analysis tools:

• https://github.com/hallvaaw/awesome-biological-image-analysis