{"name":"senoquant","display_name":"senoquant","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"senoquant.make_widget","title":"SenoQuant","python_name":"senoquant._widget:SenoQuantWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"senoquant.reader","title":"SenoQuant reader","python_name":"senoquant._reader:get_reader","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"senoquant.reader","filename_patterns":["*.czi","*.dv","*.r3d","*.264","*.265","*.3fr","*.3g2","*.a64","*.imt","*.mcidas","*.pcx","*.spider","*.xvthumb","*.adp","*.amr","*.amv","*.apng","*.arw","*.asf","*.avc","*.avi","*.avs","*.avs2","*.bay","*.bif","*.bmp","*.cdg","*.cgi","*.cif","*.ct","*.dcr","*.dib","*.dip","*.dng","*.dnxhd","*.dvd","*.erf","*.exr","*.fff","*.gif","*.icb","*.if","*.iiq","*.ism","*.jif","*.jfif","*.jng","*.jp2","*.jpg","*.mov","*.mp4","*.mpo","*.msp","*.pdf","*.png","*.ppm","*.ps","*.zif","*.lif","*.nd2","*.ome.tiff","*.tiff","*.ome.tif","*.tif","*.zarr","*.sldy","*.dir"],"accepts_directories":false}],"writers":null,"widgets":[{"command":"senoquant.make_widget","display_name":"SenoQuant","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"senoquant","version":"1.0.0b5","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"napari plugin for spatial quantification of senescence markers in tissue imaging","description":"# SenoQuant\n\n![tests](https://github.com/HaamsRee/senoquant/actions/workflows/tests.yml/badge.svg)\n[![PyPI version](https://badge.fury.io/py/senoquant.svg)](https://badge.fury.io/py/senoquant)\n[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)\n[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)\n\nSenoQuant is a versatile [napari](https://napari.org/stable/index.html) plugin designed for comprehensive, accurate,\nand unbiased spatial quantification and prediction of senescence markers\nacross diverse tissue contexts.\n\n## Features\n\n- Read microscopy formats via BioIO, including OME-TIFF, ND2, LIF, CZI, Zarr, and more.\n- Segment nuclei and cytoplasm with built-in models, including StarDist ONNX, Cellpose SAM, and morphological operations.\n- Detect punctate spots with built-in detectors.\n- Quantify marker intensity, morphology, spot counts, and spot colocalization.\n- Generate visualization outputs from quantification tables (Spatial Plot, UMAP, and Double Expression).\n- Run batch workflows across folders with multi-scene support.\n- Save/load reusable Segmentation, Spots, and Batch settings for reproducibility.\n- *Upcoming*: Integrate custom models for predicting senescence markers.\n\n## Installation\n\n### Installer (recommended)\n\n#### Windows\n\nDownload the Windows installer (`.exe`) from the [latest release](https://github.com/HaamsRee/senoquant/releases/latest).\n\n#### macOS\n\nDownload the macOS installer (`.pkg`) from the [latest release](https://github.com/HaamsRee/senoquant/releases/latest).\n\n#### Linux\n\nInstaller support for Linux is under construction.\n\n### Manual installation\n\nFor conda/pip/uv setup, see the [developer installation guide](https://haamsree.github.io/senoquant/developer/installation/).\n\n## Quick start\n\nUse the documentation workflow for the most up-to-date instructions.\n\n- Start with the [installation guide](https://haamsree.github.io/senoquant/user/installation/).\n- Follow the [quick start guide](https://haamsree.github.io/senoquant/user/quickstart/).\n- Then use tab-specific guides for [segmentation](https://haamsree.github.io/senoquant/user/segmentation/), [spots](https://haamsree.github.io/senoquant/user/spots/), [quantification](https://haamsree.github.io/senoquant/user/quantification/), [visualization](https://haamsree.github.io/senoquant/user/visualization/), [batch](https://haamsree.github.io/senoquant/user/batch/), and [settings](https://haamsree.github.io/senoquant/user/settings/).\n\n## Documentation\n\nFull documentation is available at [https://haamsree.github.io/senoquant/](https://haamsree.github.io/senoquant/).\n\n- [Installation guide](https://haamsree.github.io/senoquant/user/installation/).\n- [Quick start tutorial](https://haamsree.github.io/senoquant/user/quickstart/).\n- [Segmentation models](https://haamsree.github.io/senoquant/user/segmentation/).\n- [Spot detection](https://haamsree.github.io/senoquant/user/spots/).\n- [Quantification features](https://haamsree.github.io/senoquant/user/quantification/).\n- [Visualization tab](https://haamsree.github.io/senoquant/user/visualization/).\n- [Batch processing](https://haamsree.github.io/senoquant/user/batch/).\n- [Settings persistence](https://haamsree.github.io/senoquant/user/settings/).\n- [API reference](https://haamsree.github.io/senoquant/api/).\n\n## Development\n\nSee the [contributing guide](https://haamsree.github.io/senoquant/developer/contributing/) for development setup instructions.\n\n## How to cite\n\nIf you use SenoQuant in your research, please cite it using the metadata in `CITATION.cff`.\n\nOn GitHub, open the repository page and click `Cite this repository` in the right sidebar to copy a formatted citation.\n\n## Acknowledgements\n\nSenoQuant builds on and integrates excellent open-source projects.\n\n- [napari](https://napari.org/).\n- [StarDist](https://github.com/stardist/stardist).\n- [Cellpose](https://github.com/MouseLand/cellpose).\n- [U-FISH](https://github.com/UFISH-Team/U-FISH).\n- [BioIO](https://github.com/bioio-devs/bioio).\n","description_content_type":"text/markdown","keywords":"napari,plugin,senescence,quantification,microscopy,image analysis,segmentation,spot detection","home_page":null,"download_url":null,"author":"SenoQuant Contributors","author_email":null,"maintainer":"SenoQuant Contributors","maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 4 - Beta","Framework :: napari","Intended Audience :: Science/Research","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python :: 3","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering 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\"all\""],"requires_python":">=3.11","requires_external":null,"project_url":["Homepage, https://github.com/HaamsRee/senoquant","Documentation, https://haamsree.github.io/senoquant/","Repository, https://github.com/HaamsRee/senoquant","Bug Tracker, https://github.com/HaamsRee/senoquant/issues"],"provides_extra":["all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}