multiview-stitcher

multiview-stitcher is an open-source modular toolbox for distributed and tiled stitching of 2-3D image data in python. It is a collection of algorithms (under development) 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 and multiscale-spatial-image for image handling and dask and dask-image for chunked and distributed image processing.

Quickstart

Notebooks

Check out the example notebooks.

Napari plugin

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

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

Work in progress

WARNING: THIS IS WORK IN PROGRESS. multiview-stitcher is being developed in the open but has not been released yet.

Previous work

multiview-stitcher improves and replaces MVRegFUS.

Installation

You can install multiview-stitcher via pip from PyPI:

pip install multiview-stitcher

or from the source code in this github repository:

pip install git+https://github.com/multiview-stitcher/multiview-stitcher.git

Issues

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

Contributing

Contributions are welcome.

License

Distributed under the terms of the BSD-3 license, "multiview-stitcher" is free and open source software.