\n\n# napari-colocalization\n\n[](https://github.com/DBI-INFRA/napari-colocalization/raw/main/LICENSE)\n[](https://pypi.org/project/napari-colocalization)\n[](https://python.org)\n[](https://github.com/DBI-INFRA/napari-colocalization/actions)\n[](https://codecov.io/gh/DBI-INFRA/napari-colocalization)\n[](https://napari-hub.org/plugins/napari-colocalization)\n[](https://napari.org/stable/plugins/index.html)\n\n> ⚠️ **Under construction — pre-alpha.** APIs, UI, and outputs may change\n> without notice. Not recommended for production analysis yet; use at your\n> own risk and please report rough edges via the\n> [issue tracker](https://github.com/DBI-INFRA/napari-colocalization/issues).\n\nInteractive intensity-colocalization analysis for [napari](https://napari.org).\nPick two channels (or one multi-channel image), optionally restrict the\nanalysis to a region drawn as shapes or labels, choose your metric, and get a\nresults table plus an intensity-vs-intensity density plot.\n\n
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\n\n## Features\n\n- **Four correlation metrics**: Pearson (PCC), Spearman rank (SRCC), Li\n Intensity Correlation Quotient (ICQ), and Manders' coefficients M1/M2 (MCC).\n- **Pairwise or all-to-all** mode: analyse two grayscale layers, or every\n channel pair within a single multi-channel layer.\n- **2D and 3D** support natively (no time-series for now).\n- **Region-restricted analysis** via a Shapes or Labels layer — each non-zero\n region is reported on its own row.\n- **Manders thresholds**: choose **Costes auto** (iterative regression-based)\n or **Manual**.\n- **Interactive results**: in-widget table, density plot of the selected row,\n multi-row selection that highlights all matching shapes/labels in the viewer.\n- **CSV export** of the current table, plus **figure export** of the\n density plot (PNG / PDF / SVG / TIFF, configurable size and DPI).\n\n## Installation\n\n```bash\npip install napari-colocalization\n```\n\nIf napari isn't already installed, install both at once:\n\n```bash\npip install \"napari-colocalization[all]\"\n```\n\nFor the latest development version:\n\n```bash\npip install git+https://github.com/DBI-INFRA/napari-colocalization.git\n```\n\n## Quick start\n\n1. Launch napari.\n2. Load sample data: **File → Open Sample → napari-colocalization →\n Colocalization sample (2D)**. A 3D synthetic sample and **CBS006RBM**\n — a two-channel benchmark image from the\n [Colocalization Benchmark Source](https://colocalization-benchmark.com)\n — are also provided.\n\n
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\n\n3. Open the widget: **Plugins → Colocalization Analysis**. Two image layers\n `channel_a` and `channel_b` are auto-selected for pairwise mode.\n\n4. Click **Run**. The results table populates with a single row (the whole\n image), and the density plot below shows the intensity pairs with the\n metric values overlaid.\n\n
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\n\n5. *(Optional)* Add a Shapes layer, draw a few rectangles or polygons, set\n **Region** to *Shapes* and pick the layer. Re-run — the table now has one\n row per shape, and clicking a row highlights the matching shape in the\n viewer.\n\n
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\n\nSee [docs/usage.md](docs/usage.md) for the full walkthrough.\n\n## Documentation\n\n- **[Usage guide](docs/usage.md)** — every control in the widget, in order.\n- **[Metrics](docs/metrics.md)** — what PCC, SRCC, ICQ and MCC mean, when to use\n which, and how the Costes auto-threshold works.\n- **[Python API](docs/api.md)** — calling the pure-compute layer\n (`pearson`, `spearman`, `li_icq`, `manders`, `costes_threshold`,\n `analyse_pairwise`, `analyse_all_to_all`) from scripts or notebooks.\n\n## Related projects\n\n- [Coloc 2](https://imagej.net/plugins/coloc-2) — the reference ImageJ\n colocalization plugin; this plugin follows it in spirit.\n- [scikit-image colocalization metrics](https://scikit-image.org/docs/stable/auto_examples/applications/plot_colocalization_metrics.html)\n — the underlying implementations of PCC and Manders.\n\n## Contributing\n\nContributions are welcome. Run the test suite with:\n\n```bash\npip install -e . --group dev\npython -m pytest tests/ -v\n```\n\nPre-commit hooks (ruff lint + format, napari-plugin-checks) ship with the\nrepo:\n\n```bash\npre-commit install\npre-commit run --all-files\n```\n\nPlease keep test coverage at or above the current level when submitting a PR.\n\n## License\n\nDistributed under the terms of the [MIT](http://opensource.org/licenses/MIT)\nlicence; `napari-colocalization` is free and open-source software.\n\n## Issues\n\nFound a bug or have a feature request? Please\n[open an issue](https://github.com/DBI-INFRA/napari-colocalization/issues).\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Jesko Wagner","author_email":"35219306+jeskowagner@users.noreply.github.com","maintainer":null,"maintainer_email":null,"license":null,"classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","scikit-image","scipy","matplotlib","napari[all]; extra == \"all\""],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/jeskowagner/napari-colocalization/issues","Documentation, https://github.com/jeskowagner/napari-colocalization#README.md","Source Code, https://github.com/jeskowagner/napari-colocalization","User Support, https://github.com/jeskowagner/napari-colocalization/issues"],"provides_extra":["all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}
![\"napari-colocalization](\"https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/logo.png\"){kind=logo}
\n![\"napari-colocalization](\"https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/widget_overview.png\")
\n![\"Open](\"https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/quickstart_sample.png\")
\n ![\"napari-colocalization](\"https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/widget_shapes.png\")
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