GitBook: [master] 3 pages modified

Author: adamltyson

SUMMARY.md

@@ -56,6 +56,7 @@
 * [Installation](brainreg/installation.md)
 * [User guide](brainreg/getting-started/README.md)
   * [Registration parameters](brainreg/getting-started/registration-parameters.md)
+* [Visualisation](brainreg/visualisation.md)
 
 ## neuro
 

brainreg/introduction.md

@@ -36,3 +36,5 @@ brainreg /path/to/raw/data /path/to/output/directory -x 2 -y 2 -z 5
 For more information see [Getting started](getting-started/)
 {% endhint %}
 
+
+

brainreg/visualisation.md

@@ -0,0 +1,20 @@
+---
+description: How to look at the registration results
+---
+
+# 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)
+