brainglobe-registration

Registration to a BrainGlobe atlas using Elastix

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A napari plugin for registering images to a BrainGlobe atlas.

Usage

1. Open napari.
2. Install the plugin with pip install git+https://github.com/brainglobe/brainglobe-registration.git.
3. Open the widget by selecting Plugins > BrainGlobe Registration in the napari menu bar near the top left of the window. The BrainGlobe Registration plugin will appear on the right hand side of the napari window.
4. Open the image you want to register in napari (a sample 2D image can be found by selecting File > Open Sample > Sample Brain Slice).
5. Select the atlas you want to register to from the dropdown menu. The atlas will appear in the napari viewer. Select the approximate Z slice of the atlas that you want to register to, using the slider at the bottom of the napari viewer.
6. Adjust the sample image to roughly match the atlas image. You can do this by adjusting X and Y translation as well as rotating around the centre of the image. You can overlay the two images by toggling Grid mode in the napari viewer (Ctrl+G). You can then adjust the color map and opacity of the atlas image to make manual alignment easier. The sample image can be reset to its original position and orientation by clicking Reset Image in the BrainGlobe Registration plugin window.
7. Select the transformations you want to use from the dropdown menu. Set the transformation type to empty to remove a step. Select from one of the three provided default parameter sets (elastix, ARA, or IBL). Customise the parameters further in the Parameters tab.
8. Click Run to register the image. The registered image will appear in the napari viewer.

Installation

We strongly recommend to use a virtual environment manager (like conda or venv). 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.

[WIP] You can install brainglobe-registration via pip:

pip install brainglobe-registration

To install latest development version :

pip install git+https://github.com/brainglobe/brainglobe-registration.git

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

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

Issues

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

Acknowledgements

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.