brainglobe-stitch
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.
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.
3 maintainers
Metadata
3 maintainers
Release files for brainglobe-stitch 0.0.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| brainglobe_stitch-0.0.1.tar.gz | 18.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| brainglobe_stitch-0.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 35.7 kB
Release files / brainglobe_stitch-0.0.1.tar.gz
| Download URL | brainglobe_stitch-0.0.1.tar.gz |
|---|---|
| Size | 18.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.11.8
|
Release files / brainglobe_stitch-0.0.1-py3-none-any.whl
| Download URL | brainglobe_stitch-0.0.1-py3-none-any.whl |
|---|---|
| Size | 17.4 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.11.8
|
