QuPath is purpose-built for gigapixel whole-slide images common in pathology. It handles cell detection, tissue classification and biomarker scoring at scale.
Highlights
- Efficient tiling and visualization of multi-gigabyte slides.
- Cell and nucleus detection, positive-cell scoring and tissue segmentation.
- Scriptable in Groovy; integrates deep-learning models including StarDist and Cellpose.
Related tools
Open source
Bioimage Analysis
Fiji / ImageJ
"Fiji Is Just ImageJ" — the classic bioimage analysis platform
Desktop app
Open source
Bioimage Analysis
StarDist
Star-convex object detection for nuclei segmentation
Python libraryDesktop app
Open source
Bioimage Analysis
Cellpose
Generalist deep-learning cell and nucleus segmentation
Python libraryCommand lineDesktop app