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Add instructions for exporting to brainrender from the brainmapper widget #235

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Aug 2, 2024
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Add instructions for exporting to brainrender from the brainmapper widget #235

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6 changes: 5 additions & 1 deletion docs/source/documentation/brainglobe-utils/transform-widget.md
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Expand Up @@ -57,6 +57,7 @@ can be loaded by dragging and dropping them onto the napari window.
4. Select the `Points layer` and `Raw data layer`
5. Click `Transform points` and when prompted, select your brainreg output directory


## Results

### Transformed points
Expand All @@ -67,11 +68,14 @@ realigned to match the atlas. This is saved for completeness, but likely is not
- `Points in atlas space` - this is the points layer, but each point is transformed to the atlas space.
Importantly, this is defined at the resolution of the atlas. These points may need to be scaled up to micron space
(i.e. by multiplying the coordinates by the resolution) to visualise in tools such as
[brainrender](/documentation/brainrender/index).
[brainrender](/documentation/brainrender/index) (see below).

These layers can be saved to disk with any appropriate napari plugin, such as
[brainglobe-napari-io](https://www.napari-hub.org/plugins/brainglobe-napari-io).

To export your transformed points for visualisation in [brainrender](/documentation/brainrender/index), click the
`Export to brainrender` button, and choose a filename (ending in `.npy`). This file can be visualised in `brainrender`
by following the [visualising your data in brainrender tutorial](/tutorials/brainmapper/visualising-your-data-in-brainrender).

### Numerical results
#### Points summary
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2 changes: 2 additions & 0 deletions docs/source/tutorials/transform-cells-atlas.md
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Expand Up @@ -55,6 +55,8 @@ containing a more detailed version of the table.
containing the coordinates (in image and atlas space) and atlas region for every point for use in other analyses.
15. Select the `Points in atlas space` layer. This is the same as the `Points` layer, but each point has been moved to
its position within the atlas (in voxel space). This can be saved to disk using any compatible plugin.
15. Click on `Export to brainrender`, choose a directory, and call the file `points.npy`. This will save a file
that can be visualised [using brainrender](/tutorials/brainmapper/visualising-your-data-in-brainrender).

:::{hint}
Saving points layers with an `.xml` file extension will save the points layer to the BrainGlobe format, and these can
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