napari-vipp

napari-vipp is a napari-native visual image-processing pipeline builder for bioimage analysis. Build a typed node graph, inspect intermediate images and tables, tune parameters, save the workflow, and run the same operations without hiding axis or physical-scale metadata.

Alpha software: expect breaking workflow and parameter changes. Validate outputs on representative data before scientific interpretation or publication.

Install And Open

VIPP requires Python 3.12 or newer. If napari is not already installed, install it with a Qt backend at the same time:

python -m pip install "napari[pyqt6]"
python -m pip install --pre napari-vipp
napari

The --pre flag is required while VIPP is published as an alpha release. It is kept on the VIPP command so napari itself can continue to resolve to a stable release.

In napari, open:

Plugins > VIPP Workflow (napari-vipp)

Use Open example... for a runnable workflow with synthetic data. A good first choice is Red-Channel Label Cleanup; select nodes from left to right to review their parameters, thumbnails, metadata, and outputs.

What It Supports

Most graph operations are still eager. Large z-stacks and OME-Zarr datasets therefore need deliberate cache, preview, and output choices; see the cache and memory guide.

Optional Microscope Readers

Install only the reader family you need, then restart napari:

These routes are an experimental foundation: axes and common metadata are normalized where the source reader exposes them, but format-specific coverage still needs validation against a broader corpus of real acquisition files.

Workflow Basics

1. Add or select an Image Source for a napari layer, file, or bundled sample.
2. Add nodes from the palette and connect compatible output and input ports.
3. Select a node to tune parameters and inspect its output metadata.
4. Click Calculate for manual/cached nodes such as measurements and deconvolution.
5. Pin important image outputs into napari for full-resolution comparison.
6. Save the graph with Save workflow....
7. Add Batch Output nodes before Run batch... when exact saved outputs matter.

Workflow JSON stores the graph and optional VIPP UI state, not cached pixels or tables. Export Python... emits direct calls to the headless operation and I/O functions; it does not reproduce interactive caches or full runtime metadata propagation. See the user guide for details and caveats.

Documentation

• Documentation index
• User guide
• Image import and export
• Example workflow index
• Measurement workflows
• Operator tips
• Developer notes
• Current planning and roadmap

Development

Create a local environment and install the development dependencies:

python -m venv .venv
.venv\Scripts\Activate.ps1
python -m pip install -e ".[dev]"

Run the required checks:

python -m npe2 validate src/napari_vipp/napari.yaml
python -m ruff check .
python -m pytest

Launch a development instance with python scripts/launch_vipp_sample.py. The architecture reference explains the graph, metadata, execution, persistence, and UI boundaries.

Contributions are welcome. Read CONTRIBUTING.md before opening a pull request, use SUPPORT.md for help and issue-reporting guidance, and report suspected vulnerabilities privately through SECURITY.md. All project interactions follow the Code of Conduct.

Roadmap

The current public alpha is 0.11.0a2. This patch alpha hardens workflow restoration, generated Python, output-path validation, example launching, and saved table-column state, and adds cross-platform CI and release-readiness guidance. The next planned milestone focuses on saved batch configuration and per-item provenance, followed by scalable OME-Zarr previews and broader scientific validation. See planning.md for the maintained release order and evidence gates.

Citation, Acknowledgement, And License

If VIPP contributes to your work, acknowledge napari-vipp and link to the project repository. Citation metadata is available in CITATION.cff; a DOI or manuscript citation can be added when available.

napari-vipp is distributed under the BSD 3-Clause License. See LICENSE for the full terms.