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Since October 1, 2024, this version is no longer actively maintained and will not be updated. New plugins and plugin updates will continue to be listed.

BrainGlobe Stitch

brainglobe-stitch

A tool to stich large tiled datasets generated by the mesoSPIM.

    Stitching tiled 3D light-sheet data in napari

    Stitching a mouse brain acquired at a resolution of 4.06 µm/px, 4.06 µm/px, 5 µm/px using 4 tiles


    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.

    Installation

    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.

    Seeking help or contributing

    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.

    Citation

    If you find this package useful, please make sure to 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

    License

    Distributed under the terms of the BSD-3 license, "brainglobe-stitch" is free and open source software

    Acknowledgements

    This napari plugin was generated with Cookiecutter using napari's cookiecutter-napari-plugin template and the Neuroinformatics Unit's template.

    Version:

    • 0.0.1

    Last updated:

    • 16 October 2024

    First released:

    • 16 October 2024

    License:

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 6
    • Forks: 0
    • Issues + PRs: 3

    Python versions supported:

    Operating system:

    Requirements:

    • napari>=0.4.18
    • brainglobe-utils>=0.3.4
    • h5py
    • napari-ome-zarr
    • ome-zarr
    • zarr
    • numpy
    • qtpy
    • tifffile