A plugin to add compatibility with Tissuumaps
Project description
🏝 napari-tissuumaps 🧫
A Napari plugin to add compatibility with 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
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
choose a filename with a .tmap
extension. It will create a folder containing all the
necessary files for TissUUmaps.
📚 Documentation
Install pdoc with pip install pdoc
and run the docs/generate_doc.sh
script from the root. It will generate a static website that contains the documentation in the docs
folder.
👩💻 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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