napari-colocalization 0.1.3__tar.gz

napari_colocalization-0.1.3/.copier-answers.yml

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+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: v2.1.1
+_src_path: https://github.com/napari/napari-plugin-template
+display_name: Colocalization
+email: ''
+full_name: Jesko Wagner
+github_repository_url: https://github.com/jeskowagner/napari-colocalization
+github_username_or_organization: jeskowagner
+include_reader_plugin: false
+include_sample_data_plugin: true
+include_widget_plugin: true
+include_writer_plugin: false
+install_dependabot: false
+install_precommit: true
+license: MIT
+module_name: napari_colocalization
+plugin_name: napari-colocalization
+short_description: Colocalization analysis of multi-channel images

napari_colocalization-0.1.3/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: "\U0001F41B Bug Report"
+description: Report a bug encountered while using napari-colocalization
+labels:
+  - "bug"
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to report this issue! 🙏🏼
+
+        Please fill out the sections below to help us reproduce the problem.
+
+  - type: textarea
+    id: bug-report
+    attributes:
+      label: "\U0001F41B Bug Report"
+      description: "Please provide a clear and concise description of the bug."
+      placeholder: "What went wrong? What did you expect to happen?"
+    validations:
+      required: true
+
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: "\U0001F4A1 Steps to Reproduce"
+      description: "Please provide a minimal code snippet or list of steps to reproduce the bug."
+      placeholder: |
+        1. Go to '...'
+        2. Click on '....'
+        3. Scroll down to '....'
+        4. See error
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: "\U0001F4A1 Expected Behavior"
+      description: "Please provide a clear and concise description of what you expected to happen."
+      placeholder: "What did you expect to happen?"
+
+  - type: textarea
+    id: environment
+    attributes:
+      label: "\U0001F30E Environment"
+      description: |
+        Please provide detailed information regarding your environment. Please paste the output of `napari --info` here or copy  the information from the "napari info" dialog in the napari Help menu.
+
+        Otherwise, please provide information regarding your operating system (OS), Python version, napari version, Qt backend and version, Qt platform, method of installation, and any other relevant information related to your environment.
+
+
+      placeholder: |
+        napari: 0.5.0
+        Platform: macOS-13.2.1-arm64-arm-64bit
+        System: MacOS 13.2.1
+        Python: 3.11.4 (main, Aug 7 2023, 20:34:01) [Clang 14.0.3 (clang-1403.0.22.14.1)]
+        Qt: 5.15.10
+        PyQt5: 5.15.10
+        NumPy: 1.25.1
+        SciPy: 1.11.1
+        Dask: 2023.7.1
+        VisPy: 0.13.0
+        magicgui: 0.7.2
+        superqt: 0.5.4
+        in-n-out: 0.1.8
+        app-model: 0.2.0
+        npe2: 0.7.2
+
+        OpenGL:
+        - GL version: 2.1 Metal - 83
+        - MAX_TEXTURE_SIZE: 16384
+
+        Screens:
+        - screen 1: resolution 1512x982, scale 2.0
+
+        Settings path:
+        - /Users/.../napari/napari_5c6993c40c104085444cfc0c77fa392cb5cb8f56/settings.yaml
+    validations:
+      required: true
+
+  - type: textarea
+    id: additional-context
+    attributes:
+        label: "\U0001F4A1 Additional Context"
+        description: "Please provide any additional information or context regarding the problem here."
+        placeholder: "Add any other context about the problem here."

napari_colocalization-0.1.3/.github/ISSUE_TEMPLATE/documentation.md

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+---
+name: "\U0001F4DA Documentation"
+about: Report an issue with napari-colocalization documentation
+title: ''
+labels: documentation
+assignees: ''
+
+---
+
+## 📚 Documentation
+<!-- A clear and concise description of the documentation that needs to be created/updated -->

napari_colocalization-0.1.3/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "\U0001F680 Feature Request"
+about: Submit a proposal/request for a new napari-colocalization feature
+title: ''
+labels: feature
+assignees: ''
+
+---
+
+## 🚀 Feature
+<!-- A clear and concise description of the feature proposal -->
+
+## Motivation
+
+<!-- Please outline the motivation for the proposal. Is your feature request related to a problem? e.g., I'm always frustrated when [...]. If this is related to another GitHub issue, please link here too -->
+
+## Pitch
+
+<!-- A clear and concise description of what you want to happen. -->
+
+## Alternatives
+
+<!-- A clear and concise description of any alternative solutions or features you've considered, if any. -->
+
+## Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->

napari_colocalization-0.1.3/.github/ISSUE_TEMPLATE/task.md

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+---
+name: "\U0001F9F0 Task"
+about: Maintenance, follow-ups, and other defined to-do items
+title: ''
+labels: task
+assignees: ''
+
+---
+
+## 🧰 Task
+<!-- A clear and concise description of the task -->

napari_colocalization-0.1.3/.github/PULL_REQUEST_TEMPLATE.md

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+# References and relevant issues
+<!-- What relevant resources were used in the creation of this PR?
+If this PR addresses an existing issue on the repo,
+please link to that issue here as "Closes #(issue-number)"
+If this PR depends on another PR/issue (even in another repo),
+please link to it with "Depends on #PR-number" or "Depends on org/repo#PR-number"
+-->
+
+# Description
+<!-- What does this pull request (PR) do? Is it a new feature, a bug fix,
+an improvement, or something else? Why is it necessary? If relevant, please add
+a screenshot or a screen capture: "An image is worth a thousand words!" -->

napari_colocalization-0.1.3/.github/workflows/docs.yml

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+name: docs
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - 'src/napari_colocalization/**'
+      - 'README.md'
+      - '.github/workflows/docs.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: write   # mkdocs gh-deploy pushes to gh-pages
+
+concurrency:
+  group: docs-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0   # mkdocs gh-deploy needs full history
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: pip
+
+      - name: Install package and docs dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # Install the package itself so mkdocstrings can import
+          # napari_colocalization and read its docstrings.
+          python -m pip install . --group docs
+
+      - name: Configure Git for gh-deploy
+        run: |
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+      - name: Build and deploy to gh-pages
+        run: mkdocs gh-deploy --force --clean --verbose

napari_colocalization-0.1.3/.github/workflows/test_and_deploy.yml

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+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+      - npe2
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+      - npe2
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 30
+    permissions:
+      id-token: write  # needed for codecov OIDC authentication
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup python
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: "true"
+      - name: Install Windows OpenGL
+        uses: pyvista/setup-headless-display-action@v4.3
+        with:
+          qt: true
+          wm: herbstluftwm
+
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      # and
+      # tox-conda: https://github.com/tox-dev/tox-conda
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        run: uvx --with tox-gh-actions tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v6
+        with:
+          use_oidc: true  # reliable tokenless codecov uploads
+
+  build-and-inspect-package:
+    name: Build & inspect package.
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  deploy:
+    needs: [test, build-and-inspect-package]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    permissions:
+      id-token: write
+    steps:
+      - name: Download built artifact to dist/
+        uses: actions/download-artifact@v8
+        with:
+          name: Packages
+          path: dist
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

napari_colocalization-0.1.3/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py

napari_colocalization-0.1.3/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml # checks for correct yaml syntax for github actions ex.
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.6
+    hooks:
+      - id: ruff-check
+      - id: ruff-format
+  - repo: https://github.com/napari/napari-plugin-checks
+    rev: v0.3.0
+    hooks:
+      - id: napari-plugin-checks

napari_colocalization-0.1.3/LICENSE

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+
+The MIT License (MIT)
+
+Copyright (c) 2026 Jesko Wagner
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

napari_colocalization-0.1.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: napari-colocalization
+Version: 0.1.3
+Summary: Colocalization analysis of multi-channel images
+Author: Jesko Wagner
+Author-email: 35219306+jeskowagner@users.noreply.github.com
+License-Expression: MIT
+Project-URL: Bug Tracker, https://github.com/jeskowagner/napari-colocalization/issues
+Project-URL: Documentation, https://github.com/jeskowagner/napari-colocalization#README.md
+Project-URL: Source Code, https://github.com/jeskowagner/napari-colocalization
+Project-URL: User Support, https://github.com/jeskowagner/napari-colocalization/issues
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: magicgui
+Requires-Dist: qtpy
+Requires-Dist: scikit-image
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Dynamic: license-file
+
+<p align="center">
+  <!-- TODO: replace with final logo -->
+  <img src="https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/logo.png" alt="napari-colocalization logo" width="160"/>
+</p>
+
+# napari-colocalization
+
+[![License MIT](https://img.shields.io/pypi/l/napari-colocalization.svg?color=green)](https://github.com/DBI-INFRA/napari-colocalization/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-colocalization.svg?color=green)](https://pypi.org/project/napari-colocalization)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-colocalization.svg?color=green)](https://python.org)
+[![tests](https://github.com/DBI-INFRA/napari-colocalization/workflows/tests/badge.svg)](https://github.com/DBI-INFRA/napari-colocalization/actions)
+[![codecov](https://codecov.io/gh/DBI-INFRA/napari-colocalization/branch/main/graph/badge.svg)](https://codecov.io/gh/DBI-INFRA/napari-colocalization)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-colocalization)](https://napari-hub.org/plugins/napari-colocalization)
+[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+
+> ⚠️ **Under construction — pre-alpha.** APIs, UI, and outputs may change
+> without notice. Not recommended for production analysis yet; use at your
+> own risk and please report rough edges via the
+> [issue tracker](https://github.com/DBI-INFRA/napari-colocalization/issues).
+
+Interactive intensity-colocalization analysis for [napari](https://napari.org).
+Pick two channels (or one multi-channel image), optionally restrict the
+analysis to a region drawn as shapes or labels, choose your metric, and get a
+results table plus an intensity-vs-intensity scatter plot — all without leaving
+napari.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/widget_overview.png" alt="napari-colocalization widget" width="780"/>
+</p>
+
+## Features
+
+- **Three correlation metrics**: Pearson (PCC), Spearman rank (SRCC), and
+  Manders' coefficients M1/M2 (MCC).
+- **Pairwise or all-to-all** mode: analyse two grayscale layers, or every
+  channel pair within a single multi-channel layer.
+- **2D and 3D** support natively (no time-series for now).
+- **Region-restricted analysis** via a Shapes or Labels layer — each non-zero
+  region is reported on its own row.
+- **Manders thresholds**: choose **Costes auto** (iterative regression-based)
+  or **Manual**.
+- **Interactive results**: in-widget table, scatter plot of the selected row,
+  multi-row selection that highlights all matching shapes/labels in the viewer.
+- **CSV export** of the current table.
+
+## Installation
+
+```bash
+pip install napari-colocalization
+```
+
+If napari isn't already installed, install both at once:
+
+```bash
+pip install "napari-colocalization[all]"
+```
+
+For the latest development version:
+
+```bash
+pip install git+https://github.com/DBI-INFRA/napari-colocalization.git
+```
+
+## Quick start
+
+1. Launch napari.
+2. Load sample data: **File → Open Sample → napari-colocalization →
+   Colocalization sample (2D)** (a 3D sample is also provided).
+
+   <p align="center">
+     <img src="https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/quickstart_sample.png" alt="Open Sample menu" width="520"/>
+   </p>
+
+3. Open the widget: **Plugins → Colocalization Analysis**. Two image layers
+   `channel_a` and `channel_b` are auto-selected for pairwise mode.
+
+4. Click **Run**. The results table populates with a single row (the whole
+   image), and the scatter plot below shows the intensity pairs with the
+   metric values overlaid.
+
+   <p align="center">
+     <img src="https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/quickstart_run.png" alt="Run result" width="780"/>
+   </p>
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/widget_overview.png" alt="napari-colocalization widget" width="780"/>
+</p>
+
+5. *(Optional)* Add a Shapes layer, draw a few rectangles or polygons, set
+   **Region** to *Shapes* and pick the layer. Re-run — the table now has one
+   row per shape, and clicking a row highlights the matching shape in the
+   viewer.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/DBI-INFRA/napari-colocalization/main/docs/img/widget_shapes.png" alt="napari-colocalization widget" width="780"/>
+</p>
+
+See [docs/usage.md](docs/usage.md) for the full walkthrough.
+
+## Documentation
+
+- **[Usage guide](docs/usage.md)** — every control in the widget, in order.
+- **[Metrics](docs/metrics.md)** — what PCC, SRCC and MCC mean, when to use
+  which, and how the Costes auto-threshold works.
+- **[Python API](docs/api.md)** — calling the pure-compute layer
+  (`pearson`, `spearman`, `manders`, `costes_threshold`,
+  `analyse_pairwise`, `analyse_all_to_all`) from scripts or notebooks.
+
+## Related projects
+
+- [Coloc 2](https://imagej.net/plugins/coloc-2) — the reference ImageJ
+  colocalization plugin; this plugin follows it in spirit.
+- [scikit-image colocalization metrics](https://scikit-image.org/docs/stable/auto_examples/applications/plot_colocalization_metrics.html)
+  — the underlying implementations of PCC and Manders.
+
+## Contributing
+
+Contributions are welcome. Run the test suite with:
+
+```bash
+pip install -e . --group dev
+python -m pytest tests/ -v
+```
+
+Pre-commit hooks (ruff lint + format, napari-plugin-checks) ship with the
+repo:
+
+```bash
+pre-commit install
+pre-commit run --all-files
+```
+
+Please keep test coverage at or above the current level when submitting a PR.
+
+## License
+
+Distributed under the terms of the [MIT](http://opensource.org/licenses/MIT)
+licence; `napari-colocalization` is free and open-source software.
+
+## Issues
+
+Found a bug or have a feature request? Please
+[open an issue](https://github.com/DBI-INFRA/napari-colocalization/issues).