multiview-stitcher

multiview-stitcher is an open-source modular toolbox for distributed and tiled stitching of 2-3D image data in python. It is an extensible framework including a collection of algorithms to register and fuse small and large datasets from multi-positioning and multi-view light sheet microscopy, as well as other modalities such as correlative cryo-EM datasets.

For visualization, the associated napari-stitcher provides visualization functionality using the Napari viewer, including a standalone widget.

With a focus on interoperability and integration with existing tools and the ecosystem, the package intends to integrate as tightly as possible with the NGFF specification.

It leverages xarray in combination with spatial-image classes for image metadata handling and dask (and dask-image) for chunked and distributed image processing.

multiview-stitcher as a modular framework for registration and fusion

While multiview-stitcher contains a set of built-in functions for stitching, it is also possible to extend the package with custom functions. This can be useful for adding new registration algorithms, fusion methods, or other functionality. Have a look at the extension API documentation for more information.

Napari plugin

There's an associated napari plugin: napari-stitcher.

Previous work

multiview-stitcher improves and replaces MVRegFus.

Note

multiview-stitcher is a work in progress. The API is not yet stable.