deploy: b4fccd9

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b5b189af0a7a239d382d707930ac8171
+config: f4a15c9d50ffe4d9bb9ab4312462a6ee
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/tutorials/index.md.txt

@@ -31,6 +31,14 @@ Whole brain cell detection and registration
 :link-type: doc
 Analyze and visualize bulk fluorescence tracing data
 :::
+
+:::{grid-item-card} {fas}`brain;sd-text-primary` Atlas visualisation
+:img-bottom: images/visualise-atlas-napari.png
+:link: visualise-atlas-napari
+:link-type: doc
+Visualise atlas data in napari
+:::
+
 ::::
 
 ```{toctree}

_sources/tutorials/visualise-atlas-napari.md.txt

@@ -0,0 +1,38 @@
+## Visualise an atlas in napari
+
+BrainGlobe atlases are made of different components. These include the annotations image, the (default) reference image, 3D brain region meshes and, optionally, additional reference images. In this tutorial, you will use `brainrender-napari` to visualise each of these components in the 3D viewer napari through a series of simple clicks. The [`mpin_zfish_1um` zebrafish brain atlas](https://doi.org/10.1016/j.neuron.2019.04.034) will serve as an example. 
+
+:::{note}
+You will need `napari` installed on your computer - please follow [`napari`'s installation instructions to do so](https://napari.org/stable/tutorials/fundamentals/installation.html).
+:::
+
+1. Open `napari`.
+2. Install `brainrender-napari` by selecting `Plugins > Install/Uninstall plugins` and searching for `brainrender-napari` in the searchbox. Then click on the `Install` button.
+3. Open the `brainrender` widget by selecting `Plugins > Brainrender (brainrender-napari)` in the napari menu bar near the top left of the window. 
+![brainrender widget](./images/brainrender-napari/plugin-menu-brainrender-napari.png)
+**The brainrender widget appears on the right hand side of the window.**
+
+4. In the `brainrender` widget's `Atlas table view` section, double-click the row which contains the `mpin_zfish_1um` atlas.
+![brainrender widget with added annotations](./images/brainrender-napari/added-brainrender-napari.png)
+**You have now added the annotations image and the default reference image to napari: They appear as layers in the napari layers list on the lower left of the window. A `3D Brain region meshes` section appears below the `Atlas table view` section.**
+
+:::{note}
+If you haven't downloaded the atlas before, the plugin will prompt you to download it (click yes). It may take a long time
+(depending on your internet speed) so please be patient. Once downloaded, double click again to view the atlas.
+:::
+
+5. Toggle the napari display from 2D to 3D by pressing the button with the square icon on the lower left of the window.
+![brainrender widget with 3d display](./images/brainrender-napari/toggle-ndisplay-brainrender-napari.png)
+**The annotations image should now be displayed in 3D.**
+6. Navigate the brain region tree in the `3D Brain region meshes` section by opening "forebrain". Double-click on `telencephalon`.
+![brainrender widget with region mesh](./images/brainrender-napari/add-region-brainrender-napari.png)
+ **You have now added a 3D brain region mesh layer, which appears as a mesh in the viewer and as a new layer in the layers list.**
+7. Back in the "Atlas table view" section, right-click on the `mpin_zfish_1um` row. In the menu that appears, select `GAD1b`.
+![brainrender widget with additional reference](./images/brainrender-napari/additional-reference-brainrender-napari.png)
+**You have now added an additional reference image, which appears as a grey scale image in the viewer and as a new layer in the layers list.**
+
+You have now added all possible kinds of BrainGlobe atlas components (annotations image, reference image, 3D brain region mesh, additional reference) to napari - well done! You can now add any of the other atlases listed in the `Atlas table view` if you like (note that not all atlases have additional references!). 
+
+:::{note}
+Hover over any of the elements in the `brainrender` widget to get additional hints about how to use them!
+:::

tutorials/index.html

@@ -466,6 +466,16 @@ <h1>Tutorials<a class="headerlink" href="#tutorials" title="Permalink to this he
 <img alt="" class="sd-card-img-bottom" src="../_images/bulkaxons.png" />
 <a class="sd-stretched-link reference internal" href="tracing-tracking.html"><span class="doc"></span></a></div>
 </div>
+<div class="sd-col sd-d-flex-row docutils">
+<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
+<div class="sd-card-body docutils">
+<div class="sd-card-title sd-font-weight-bold docutils">
+<span class="fas fa-brain sd-text-primary"></span> Atlas visualisation</div>
+<p class="sd-card-text">Visualise atlas data in napari</p>
+</div>
+<img alt="" class="sd-card-img-bottom" src="../_images/visualise-atlas-napari.png" />
+<a class="sd-stretched-link reference internal" href="visualise-atlas-napari.html"><span class="doc"></span></a></div>
+</div>
 </div>
 </div>
 <div class="toctree-wrapper compound">