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adamltyson committed Aug 13, 2020
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Expand Up @@ -104,3 +104,17 @@ Full command-line arguments are available with `brainreg -h`, but please
[get in touch](mailto:adam.tyson@ucl.ac.uk?subject=brainreg) if you have any questions.


### Visualisation

brainreg comes with a plugin ([napari-brainreg](https://github.com/brainglobe/napari-brainreg)) for [napari](https://github.com/napari/napari)

To visualise your data, open napari and drag your brainreg output directory (the one with the log file) onto the napari window.

Various images should then open, including:
* `Image (downsampled)` - the image used for registration
* `Annotations` - the atlas labels, warped to your sample brain
* `Boundaries` - the boundaries of the atlas regions

If you downsampled additional channels, these will also be loaded.

![process](https://raw.githubusercontent.com/brainglobe/napari-brainreg/master/resources/napari-brainreg.png)

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