napari-tissuumaps

A plugin to export Napari projects to TissUUmaps.


    Learn more:

    • Documentation
    • Support site
    • Report issues

    Source code:

    • Information not submitted

    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.

    Version:

    • 1.1.2

    Release date:

    • 05 August 2022

    First released:

    • 02 September 2021

    License:

    • MIT

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 0
    • Forks: 0
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • numpy

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