Restructure introductory registration plugin (#90)

* Reorganise tutorials

* rename registration tutorial

* Restructure basic registration tutorial

* Rename tutorial sections

docs/source/tutorials/index.md

@@ -1,15 +1,28 @@
 # Tutorials
 
-
+## Getting started
 ::::{grid} 1 2 2 3
 :gutter: 3
 
+:::{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
+:::
+
 :::{grid-item-card} {fas}`brain;sd-text-primary` 3D registration
 :img-bottom: images/brainreg.png
-:link: brainreg
+:link: tutorial-whole-brain-registration
 :link-type: doc
 Registering a whole-brain dataset to an atlas.
 :::
+::::
+
+## Specific applications
+::::{grid} 1 2 2 3
+:gutter: 3
+
 
 :::{grid-item-card} {fas}`brain;sd-text-primary` Probe segmentation
 :img-bottom: images/probes.png
@@ -18,12 +31,6 @@ Registering a whole-brain dataset to an atlas.
 Analysis of silicon probe tracks (e.g. Neuropixels)
 :::
 
-:::{grid-item-card} {fas}`brain;sd-text-primary` Cell detection
-:img-bottom: images/cellfinder.png
-:link: cellfinder-cli/index
-:link-type: doc
-Whole brain cell detection and registration
-:::
 
 :::{grid-item-card} {fas}`brain;sd-text-primary` Bulk tracing analysis
 :img-bottom: images/bulkaxons.png
@@ -32,11 +39,11 @@ Whole brain cell detection and registration
 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
+:::{grid-item-card} {fas}`brain;sd-text-primary` Cell detection
+:img-bottom: images/cellfinder.png
+:link: cellfinder-cli/index
 :link-type: doc
-Visualise atlas data in napari
+Whole brain cell detection and registration
 :::
 
 ::::
@@ -45,9 +52,10 @@ Visualise atlas data in napari
 :maxdepth: 2
 :caption: Index
 :hidden:
-brainreg
+visualise-atlas-napari
+tutorial-whole-brain-registration
 silicon-probe-tracking
-cellfinder-cli/index
 tracing-tracking
-visualise-atlas-napari
-```
+cellfinder-cli/index
+
+```

docs/source/tutorials/tutorial-whole-brain-registration.md

@@ -0,0 +1,62 @@
+# Registering a whole-brain image to an atlas
+
+In this tutorial, you will use the [brainreg](/documentation/brainreg) plugin for [napari](https://napari.org) to 
+register (align) a whole-mouse brain image to a reference atlas.
+
+The focus of this tutorial is simply to successfully register a single image.
+Optimising brainreg for specific applications will be covered separately. 
+
+:::{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 `brainreg-napari` by selecting `Plugins > Install/Uninstall plugins` and searching for `brainreg-napari` in the searchbox. Then click on the `Install` button.
+3. Open the `brainreg` widget by selecting `Plugins > Atlas registration (brainreg-napari)` in the napari menu bar near the top left of the window.
+![brainreg widget](./images/brainreg-napari/plugin-menu-brainreg-napari.png)
+
+**The brainreg widget appears on the right-hand side of the window.**
+
+4. Open the sample image by selecting `File > Open Sample > Low resolution brain (brainreg-napari)`. 
+5. Make the image easier to see by adjusting the `contrast limits` in the top left section of the napari window. Moving
+the right-hand slider to the left will make the image appear brighter. 
+![loaded image](./images/brainreg-napari/image-loaded-brainreg-napari.png)
+
+**A whole mouse brain image loaded into napari.**
+
+
+6. In the plugin widget, set all the necessary parameters:
+
+* `Image layer` - Set this to the `Sample brain` image layer
+* `Atlas` - Set this to `allen_mouse_50um`
+* `Data orientation` - Set this to `psl`
+* `Voxel size (z)` - Set to 50
+* `Voxel size (x)` - Set to 40
+* `Voxel size (y)` - Set to 40
+* `Output directory` - Click `Choose directory`, and create a new directory on your machine
+
+7. Click `Run`. After 30-60 seconds, two new napari layers will be loaded, `Boundaries` and `allen_mouse_50um`.
+8. Toggle the visibility of these two layers (using the eye icon on the left of the layer name) to overlay the 
+registration results. These can be explored by zooming in/out, scrolling through the 3D data and adjusting the 
+visibility and contrast of the loaded data. 
+
+![loaded image](./images/brainreg-napari/results-brainreg-napari.png)
+
+**Registration results overlaid onto raw data.**
+
+9. At this point, registration is complete. A number of 
+[files are created in the output directory](documentation/brainreg/user-guide/output-files) that can be used for 
+downstream analysis.
+
+:::{note}
+The results are likely not perfect because (for speed and simplicity) we:
+
+* Used very low-resolution data
+* Use a low-resolution atlas
+* Left all the parameters as default (which were optimised for higher resolution atlases)
+:::
+
+
+```{hint}
+For full information on how to use brainreg, please see the [brainreg page](/documentation/brainreg/index)
+```