A selection of tools and pipelines we develop and maintain across GitHub.
Spatial & Multiplex Imaging
- CellSurvey – GPU-accelerated pipeline for spatial omics (Sopa/SpatialData)
Quality Control
- CrosstalkPy – Detect channel bleed-through in microscopy
- flag-qc – Bioimage quality control tools
Image Analysis
- 3D Nuclear Intensity Quantification – 3D nuclear intensity tools
- Object Midline Detection – Bioimage midline detection
- Cell Classifier – Machine learning for cell classification
- BRAINSAW Data Processing – BRAINSAW pipeline
- Pancreatic Tissue Integrity (QuPath) – QuPath tools for tissue assessment
Tools & Utilities
- Image Analysis Template – Project template
- Data Prospector – AI-driven dataset exploration
- BioImage Analysis Bot (biabot) – AI triage for bioimage projects
Training & Education
- Napari Tutorial – Modular napari course
- Intro to Image Analysis – Training workshop
- Reproducible Statistics – Notebooks on reproducibility