Stitching tiled 3D light-sheet data in napari
A napari plugin for stitching tiled 3D acquisitions from a mesoSPIM light-sheet microscope. The plugin utilises BigStitcher to align the tiles and napari to visualise the stitched data.
We strongly recommend to use a virtual environment manager (like conda). The installation instructions below
will not specify the Qt backend for napari, and you will therefore need to install that separately. Please see the
napari installation instructions for further advice on this.
To install latest development version:
pip install git+https://github.com/brainglobe/brainglobe-stitch.git
This plugin requires Fiji to be installed on your system. You can download Fiji here.
The BigStitcher plugin must be installed in Fiji. Please follow the instructions here.
We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the contact page of our website.
If you find this package useful, please cite it in your work:
Igor Tatarnikov, Alessandro Felder, & Adam Tyson. (2024). brainglobe/brainglobe-stitch, Zenodo. https://doi.org/10.5281/zenodo.14001001
Please also cite the original BigStitcher publication:
Hörl, D., Rojas Rusak, F., Preusser, F. et al. BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples. Nat Methods 16, 870–874 (2019). https://doi.org/10.1038/s41592-019-0501-0
Distributed under the terms of the BSD-3 license, "brainglobe-stitch" is free and open source software
This napari plugin was generated with Cookiecutter using napari's cookiecutter-napari-plugin template and the Neuroinformatics Unit's template.