napari-stitcher

A napari plugin for stitching large multi-positioning datasets in 2/3D+t using multiview-stitcher.

Image data by Arthur Michaut @ Jérôme Gros Lab @ Institut Pasteur.

Quick guide:

1. Directly stitch napari layers: Use napari to load, visualize and preposition the tiles to be stitched.
2. When working with multi-channel data, stick to the following naming convention: {tile} :: {channel}.
3. Load either all or just a subset of the layers into the plugin.
4. Choose registration options: registration channel, binning and more.
5. Stitching = registration (refining the positions, optional) + fusion (joining the tiles into a single image).
6. The registration result is shown in the viewer and the fused channels are added as new layers.

Demo

demo_3d.mp4

This demo uses the awesome napari-threedee for prepositioning the tiles. Image data: BigStitcher.

Documentation

Head over to the user guide for more details.

Installation

You can install napari-stitcher via pip:

pip install napari-stitcher

For more installation options, see the installation docs.

Contributing

Contributions are very welcome. Tests can be run with tox.

License

Distributed under the terms of the [BSD-3] license, "napari-stitcher" is free and open source software

Issues

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