napari-cellposesam 0.1.0__tar.gz

napari_cellposesam-0.1.0/.github/workflows/test_and_deploy.yml

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+# Runs tests on push/PR. On a "v*" tag, builds the package and publishes it to PyPI
+# via trusted publishing: https://docs.pypi.org/trusted-publishers/
+
+### test workflow from Talley Lambert's napari-omero! thanks!
+# https://github.com/tlambert03/napari-omero/blob/main/.github/workflows/ci.yml
+
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: tlambert03/setup-qt-libs@v1
+
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade setuptools tox tox-gh-actions
+
+      # model weights (~1.2 GB) and sample data are fetched once, with retries, and
+      # cached, so tests don't download them mid-run from flaky/slow servers
+      - name: Restore cellpose models and sample data
+        id: cp-cache
+        uses: actions/cache/restore@v6
+        with:
+          path: ~/.cellpose
+          key: cellpose-assets-v1-${{ runner.os }}
+
+      - name: Fetch cellpose models and sample data
+        if: steps.cp-cache.outputs.cache-hit != 'true'
+        shell: bash
+        run: |
+          mkdir -p ~/.cellpose/models
+          curl -fsSL --retry 5 --retry-all-errors --retry-delay 10 -o ~/.cellpose/models/cpsam https://huggingface.co/mouseland/cellpose-sam/resolve/main/cpsam
+          curl -fsSL --retry 5 --retry-all-errors --retry-delay 10 -o ~/.cellpose/data.zip https://osf.io/download/s52q3/
+          python -m zipfile -e ~/.cellpose/data.zip ~/.cellpose
+
+      - name: Save cellpose models and sample data
+        if: steps.cp-cache.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v6
+        with:
+          path: ~/.cellpose
+          key: cellpose-assets-v1-${{ runner.os }}
+
+      - name: Test with tox
+        uses: aganders3/headless-gui@v2
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Codecov
+        uses: codecov/codecov-action@v6
+
+  test-cellpose3:
+    name: cellpose v3 compat (ubuntu, py3.11)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - uses: tlambert03/setup-qt-libs@v1
+
+      - name: Install dependencies (cellpose v3 pinned)
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[testing]" "cellpose>=3,<4"
+
+      - name: Restore cellpose models and sample data
+        id: cp-cache
+        uses: actions/cache/restore@v6
+        with:
+          path: ~/.cellpose
+          key: cellpose3-assets-v1-${{ runner.os }}
+
+      - name: Fetch cellpose models and sample data
+        if: steps.cp-cache.outputs.cache-hit != 'true'
+        run: |
+          mkdir -p ~/.cellpose/models
+          for f in cyto3 size_cyto3.npy; do
+            curl -fsSL --retry 5 --retry-all-errors --retry-delay 10 -o ~/.cellpose/models/$f https://www.cellpose.org/models/$f
+          done
+          curl -fsSL --retry 5 --retry-all-errors --retry-delay 10 -o ~/.cellpose/data.zip https://osf.io/download/s52q3/
+          python -m zipfile -e ~/.cellpose/data.zip ~/.cellpose
+
+      - name: Save cellpose models and sample data
+        if: steps.cp-cache.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v6
+        with:
+          path: ~/.cellpose
+          key: cellpose3-assets-v1-${{ runner.os }}
+
+      - name: Test with pytest
+        uses: aganders3/headless-gui@v2
+        with:
+          run: pytest -v --color=yes
+        env:
+          CI: true
+
+  build:
+    name: Build distribution
+    needs: [test, test-cellpose3]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0  # setuptools_scm needs the tag history for the version
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.x"
+      - name: Build and check
+        run: |
+          python -m pip install --upgrade build twine
+          python -m build
+          twine check dist/*
+      - uses: actions/upload-artifact@v7
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/napari-cellposesam
+    permissions:
+      id-token: write  # trusted publishing
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@v1.14.2

napari_cellposesam-0.1.0/.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/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+*/_version.py

napari_cellposesam-0.1.0/.readthedocs.yaml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Only the docs toolchain is installed, not the plugin (which would pull in torch)
+python:
+  install:
+    - requirements: docs/requirements.txt

napari_cellposesam-0.1.0/LICENSE

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+
+Copyright (c) 2021, Carsen Stringer
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of cellpose-napari nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

napari_cellposesam-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: napari-cellposesam
+Version: 0.1.0
+Summary: napari plugin for cellpose and Cellpose-SAM segmentation
+Author-email: Carsen Stringer <stringerc@janelia.hhmi.org>, Jesko Wagner <35219306+jeskowagner@users.noreply.github.com>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/jeskowagner/napari-cellposesam
+Project-URL: Bug Tracker, https://github.com/jeskowagner/napari-cellposesam/issues
+Project-URL: Upstream, https://github.com/MouseLand/cellpose-napari
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Framework :: napari
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: napari>=0.6
+Requires-Dist: magicgui
+Requires-Dist: cellpose>=3
+Requires-Dist: imagecodecs
+Provides-Extra: docs
+Requires-Dist: sphinx>=3.0; extra == "docs"
+Requires-Dist: sphinxcontrib-apidoc; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: sphinx-prompt; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Provides-Extra: testing
+Requires-Dist: tox; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest-qt; extra == "testing"
+Requires-Dist: napari; extra == "testing"
+Requires-Dist: pyqt6; extra == "testing"
+Dynamic: license-file
+
+# napari-cellposesam <img src="docs/_static/favicon.ico" width="50" title="cellpose" alt="cellpose" align="right" vspace = "50">
+
+[![Documentation Status](https://readthedocs.org/projects/napari-cellposesam/badge/?version=latest)](https://napari-cellposesam.readthedocs.io/en/latest/)
+[![tests](https://github.com/jeskowagner/napari-cellposesam/actions/workflows/test_and_deploy.yml/badge.svg)](https://github.com/jeskowagner/napari-cellposesam/actions)
+[![PyPI version](https://img.shields.io/pypi/v/napari-cellposesam)](https://pypi.org/project/napari-cellposesam/)
+[![Python version](https://img.shields.io/pypi/pyversions/napari-cellposesam)](https://pypi.org/project/napari-cellposesam/)
+[![License](https://img.shields.io/pypi/l/napari-cellposesam.svg?color=green)](https://github.com/jeskowagner/napari-cellposesam/raw/main/LICENSE)
+[![website](https://img.shields.io/website?url=https%3A%2F%2Fwww.cellpose.org)](https://www.cellpose.org)
+
+A [napari] plugin for cell segmentation with [cellpose], including Cellpose-SAM (cellpose v4).
+
+This is a fork of [MouseLand/cellpose-napari](https://github.com/MouseLand/cellpose-napari), the original plugin by Carsen Stringer. It adds:
+
+- support for cellpose v4 and the Cellpose-SAM (`cpsam`) models, while still working with cellpose v3
+- z/channel axis selection for 3D and 4D images
+- fp32 inference on CPU, which is much faster than bf16 on CPUs without native bf16 support
+- an npe2 manifest and `pyproject.toml` packaging
+
+The cellpose code was written by Carsen Stringer and Marius Pachitariu. To learn about Cellpose, read the [**paper**](https://t.co/kBMXmPp3Yn?amp=1) or watch this [**talk**](https://t.co/JChCsTD0SK?amp=1).
+
+For problems with this plugin, open an [issue](https://github.com/jeskowagner/napari-cellposesam/issues). For problems with cellpose itself, open an [issue](https://github.com/MouseLand/cellpose/issues) on the cellpose repo.
+
+If you use this plugin, please cite the [cellpose paper](https://www.nature.com/articles/s41592-020-01018-x), and the Cellpose-SAM paper if you use the `cpsam` models (see the [cellpose repo](https://github.com/MouseLand/cellpose) for the reference):
+
+```bibtex
+@article{stringer2021cellpose,
+  title={Cellpose: a generalist algorithm for cellular segmentation},
+  author={Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius},
+  journal={Nature Methods},
+  volume={18},
+  number={1},
+  pages={100--106},
+  year={2021},
+  publisher={Nature Publishing Group}
+}
+```
+
+![napari-cellposesam segmenting the 2D sample image](https://raw.githubusercontent.com/jeskowagner/napari-cellposesam/main/docs/_static/gui.png)
+
+## Installation
+
+Requires Python 3.11 or newer. We recommend a fresh environment, e.g. with conda:
+
+```
+conda create -n napari-cellposesam python=3.12
+conda activate napari-cellposesam
+```
+
+Install napari and the plugin with pip:
+
+```
+pip install "napari[all]" napari-cellposesam
+```
+
+Or install the plugin from the napari plugin manager (Plugins > Install/Uninstall Plugins).
+
+To install the latest development version from GitHub:
+
+```
+pip install git+https://github.com/jeskowagner/napari-cellposesam
+```
+
+If you have issues installing cellpose, see the [cellpose installation docs](https://cellpose.readthedocs.io/en/latest/installation.html).
+
+### GPU
+
+cellpose runs on CPU, NVIDIA GPUs (CUDA) and Apple silicon (MPS). For CUDA, install a CUDA build of torch following the [PyTorch instructions](https://pytorch.org/get-started/locally/) before or after installing the plugin. The plugin uses the GPU automatically if torch can see one.
+
+### Optional: CPDINO models
+
+The CPDINO models need [DINOv3](https://github.com/facebookresearch/dinov3), which is not on PyPI and so is not installed automatically. The plugin offers to install it when you run segmentation with a CPDINO model, or install it yourself:
+
+```
+pip install git+https://github.com/facebookresearch/dinov3
+```
+
+Without it, cellpose logs a `Could not import CPDINO` warning on startup. This is harmless if you don't use those models.
+
+### Upgrading
+
+```
+pip install --upgrade napari-cellposesam cellpose
+```
+
+## Usage
+
+Open napari with the plugin docked:
+
+```
+napari -w napari-cellposesam
+```
+
+Sample data is available under File > Open Sample > napari-cellposesam.
+
+Detailed usage is described in the [documentation](https://napari-cellposesam.readthedocs.io/).
+
+## Contributing
+
+Contributions are welcome. For development, clone the repo and install it in editable mode with the test dependencies:
+
+```
+pip install -e ".[testing]"
+pytest
+```
+
+## License
+
+Distributed under the terms of the [BSD-3] license, "napari-cellposesam" is free and open source software.
+
+## Dependencies
+
+napari-cellposesam relies on:
+- [napari](https://napari.org)
+- [magicgui](https://napari.org/magicgui/)
+- [cellpose], which in turn uses [torch](https://pytorch.org/), [numpy](https://numpy.org/), [scipy](https://scipy.org/), [opencv](https://opencv.org/) and others
+
+[napari]: https://github.com/napari/napari
+[cellpose]: https://github.com/MouseLand/cellpose
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause

napari_cellposesam-0.1.0/README.md

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+# napari-cellposesam <img src="docs/_static/favicon.ico" width="50" title="cellpose" alt="cellpose" align="right" vspace = "50">
+
+[![Documentation Status](https://readthedocs.org/projects/napari-cellposesam/badge/?version=latest)](https://napari-cellposesam.readthedocs.io/en/latest/)
+[![tests](https://github.com/jeskowagner/napari-cellposesam/actions/workflows/test_and_deploy.yml/badge.svg)](https://github.com/jeskowagner/napari-cellposesam/actions)
+[![PyPI version](https://img.shields.io/pypi/v/napari-cellposesam)](https://pypi.org/project/napari-cellposesam/)
+[![Python version](https://img.shields.io/pypi/pyversions/napari-cellposesam)](https://pypi.org/project/napari-cellposesam/)
+[![License](https://img.shields.io/pypi/l/napari-cellposesam.svg?color=green)](https://github.com/jeskowagner/napari-cellposesam/raw/main/LICENSE)
+[![website](https://img.shields.io/website?url=https%3A%2F%2Fwww.cellpose.org)](https://www.cellpose.org)
+
+A [napari] plugin for cell segmentation with [cellpose], including Cellpose-SAM (cellpose v4).
+
+This is a fork of [MouseLand/cellpose-napari](https://github.com/MouseLand/cellpose-napari), the original plugin by Carsen Stringer. It adds:
+
+- support for cellpose v4 and the Cellpose-SAM (`cpsam`) models, while still working with cellpose v3
+- z/channel axis selection for 3D and 4D images
+- fp32 inference on CPU, which is much faster than bf16 on CPUs without native bf16 support
+- an npe2 manifest and `pyproject.toml` packaging
+
+The cellpose code was written by Carsen Stringer and Marius Pachitariu. To learn about Cellpose, read the [**paper**](https://t.co/kBMXmPp3Yn?amp=1) or watch this [**talk**](https://t.co/JChCsTD0SK?amp=1).
+
+For problems with this plugin, open an [issue](https://github.com/jeskowagner/napari-cellposesam/issues). For problems with cellpose itself, open an [issue](https://github.com/MouseLand/cellpose/issues) on the cellpose repo.
+
+If you use this plugin, please cite the [cellpose paper](https://www.nature.com/articles/s41592-020-01018-x), and the Cellpose-SAM paper if you use the `cpsam` models (see the [cellpose repo](https://github.com/MouseLand/cellpose) for the reference):
+
+```bibtex
+@article{stringer2021cellpose,
+  title={Cellpose: a generalist algorithm for cellular segmentation},
+  author={Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius},
+  journal={Nature Methods},
+  volume={18},
+  number={1},
+  pages={100--106},
+  year={2021},
+  publisher={Nature Publishing Group}
+}
+```
+
+![napari-cellposesam segmenting the 2D sample image](https://raw.githubusercontent.com/jeskowagner/napari-cellposesam/main/docs/_static/gui.png)
+
+## Installation
+
+Requires Python 3.11 or newer. We recommend a fresh environment, e.g. with conda:
+
+```
+conda create -n napari-cellposesam python=3.12
+conda activate napari-cellposesam
+```
+
+Install napari and the plugin with pip:
+
+```
+pip install "napari[all]" napari-cellposesam
+```
+
+Or install the plugin from the napari plugin manager (Plugins > Install/Uninstall Plugins).
+
+To install the latest development version from GitHub:
+
+```
+pip install git+https://github.com/jeskowagner/napari-cellposesam
+```
+
+If you have issues installing cellpose, see the [cellpose installation docs](https://cellpose.readthedocs.io/en/latest/installation.html).
+
+### GPU
+
+cellpose runs on CPU, NVIDIA GPUs (CUDA) and Apple silicon (MPS). For CUDA, install a CUDA build of torch following the [PyTorch instructions](https://pytorch.org/get-started/locally/) before or after installing the plugin. The plugin uses the GPU automatically if torch can see one.
+
+### Optional: CPDINO models
+
+The CPDINO models need [DINOv3](https://github.com/facebookresearch/dinov3), which is not on PyPI and so is not installed automatically. The plugin offers to install it when you run segmentation with a CPDINO model, or install it yourself:
+
+```
+pip install git+https://github.com/facebookresearch/dinov3
+```
+
+Without it, cellpose logs a `Could not import CPDINO` warning on startup. This is harmless if you don't use those models.
+
+### Upgrading
+
+```
+pip install --upgrade napari-cellposesam cellpose
+```
+
+## Usage
+
+Open napari with the plugin docked:
+
+```
+napari -w napari-cellposesam
+```
+
+Sample data is available under File > Open Sample > napari-cellposesam.
+
+Detailed usage is described in the [documentation](https://napari-cellposesam.readthedocs.io/).
+
+## Contributing
+
+Contributions are welcome. For development, clone the repo and install it in editable mode with the test dependencies:
+
+```
+pip install -e ".[testing]"
+pytest
+```
+
+## License
+
+Distributed under the terms of the [BSD-3] license, "napari-cellposesam" is free and open source software.
+
+## Dependencies
+
+napari-cellposesam relies on:
+- [napari](https://napari.org)
+- [magicgui](https://napari.org/magicgui/)
+- [cellpose], which in turn uses [torch](https://pytorch.org/), [numpy](https://numpy.org/), [scipy](https://scipy.org/), [opencv](https://opencv.org/) and others
+
+[napari]: https://github.com/napari/napari
+[cellpose]: https://github.com/MouseLand/cellpose
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause

napari_cellposesam-0.1.0/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = ../build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)