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A plugin to export Napari projects to TissUUmaps.

Project description

🏝 napari-tissuumaps 🧫

License MIT PyPI Python Version tests codecov napari hub

A plugin to export Napari projects to TissUUmaps.

This plugins adds a new writer to Napari to export projects to TissUUmaps. Exported projects can then be open on the browser or on a standalone GUI with TissUUmaps. More information and demonstrations are available on the TissUUmaps webpage.

🚀 Features

Demonstration of a project exported from Napari to TissUUmaps.

The plugin now supports:

  • Exporting images
  • Exporting labels
  • Exporting points
  • Exporting shapes, including:
    • Polygons
    • Rectangles
    • Lines
    • Paths
    • Ellipses

The plugin exports the right color for the points, shapes and labels and also saves the visibility/opacity of each layers. The shapes are exported in the GeoJSON format, the points in CSV files, and images as TIFFs.

📺 Installation

You can install napari-tissuumaps via pip:

pip install napari-tissuumaps

You can also install napari-tissumaps via napari:

In Napari, access the menubar, Plugins > Install/Uninstall Plugins. Search for napari-tissuumaps in the list and choose install, or type napari-tissuumaps in the "install by name/url, or drop file..." text area and choose install.

⛏ Usage

To export a project for TissUUmaps, access the menubar, File > Save All Layers... and type in a filename. Choose the .tmap extension in the dropdown and click on the Save button, It will create a folder containing all the necessary files for TissUUmaps.

👩‍💻 Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

⚖️ License

Distributed under the terms of the MIT license, "napari-tissuumaps" is free and open source software

🚒 Issues

If you encounter any problems, please [file an issue] along with a detailed description.

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