napari-stitcher

This plugin stitches images (napari layers) in 2/3D+t. Images can either be (pre-)aligned manually or on a grid.

Here's it's user guide and github repository. napari-stitcher uses multiview-stitcher for registration and fusion.

Overview¶

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

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¶

Link to video demo.

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