senoquant 1.0.0b5

napari plugin for spatial quantification of senescence markers in tissue imaging

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

• Read microscopy formats via BioIO, including OME-TIFF, ND2, LIF, CZI, Zarr, and more.
• Segment nuclei and cytoplasm with built-in models, including StarDist ONNX, Cellpose SAM, and morphological operations.
• Detect punctate spots with built-in detectors.
• Quantify marker intensity, morphology, spot counts, and spot colocalization.
• Generate visualization outputs from quantification tables (Spatial Plot, UMAP, and Double Expression).
• Run batch workflows across folders with multi-scene support.
• Save/load reusable Segmentation, Spots, and Batch settings for reproducibility.
• 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, visualization, batch, and settings.

Documentation

Full documentation is available at https://haamsree.github.io/senoquant/.

• Installation guide.
• Quick start tutorial.
• Segmentation models.
• Spot detection.
• Quantification features.
• Visualization tab.
• Batch processing.
• Settings persistence.
• 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.

• napari.
• StarDist.
• Cellpose.
• U-FISH.
• BioIO.