napari plugin for spatial quantification of senescence markers in tissue imaging
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Project description
SenoQuant
SenoQuant is a versatile napari plugin designed for comprehensive, accurate, and unbiased spatial quantification and prediction of senescence markers across diverse tissue contexts.
Features
- Segment nuclei and cytoplasm with built-in models, including StarDist ONNX, Cellpose SAM, and morphology-based models.
- Detect punctate spots with a U-FISH-based detector.
- Quantify marker intensity, morphology, spot counts, and spot colocalization.
- Run batch workflows across folders, including profile save/load and multi-scene support.
- Read microscopy formats via BioIO, including OME-TIFF, ND2, LIF, CZI, Zarr, and more.
- Upcoming: Integrate custom models for predicting senescence markers.
Installation
Installer (recommended)
Windows
Download the Windows installer (.exe) from the latest release.
macOS
Download the macOS installer (.pkg) from the latest release.
Linux
Installer support for Linux is under construction.
Manual installation
For conda/pip/uv setup, see the developer installation guide.
Quick start
Use the documentation workflow for the most up-to-date instructions.
- Start with the installation guide.
- Follow the quick start guide.
- Then use tab-specific guides for segmentation, spots, quantification, and batch.
Documentation
Full documentation is available at https://haamsree.github.io/senoquant/.
- Installation guide.
- Quick start tutorial.
- Segmentation models.
- Spot detection.
- Quantification features.
- Batch processing.
- API reference.
Development
See the contributing guide for development setup instructions.
How to cite
If you use SenoQuant in your research, please cite it using the metadata in CITATION.cff.
On GitHub, open the repository page and click Cite this repository in the right sidebar to copy a formatted citation.
Acknowledgements
SenoQuant builds on and integrates excellent open-source projects.
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