From 8b8c50afe981202604f50e23eef52cc627302d9d Mon Sep 17 00:00:00 2001
From: Adam Tyson <code@adamltyson.com>
Date: Wed, 16 Oct 2024 16:56:10 +0100
Subject: [PATCH] Add whole brain microscopy analysis course (#221)

Co-authored-by: alessandrofelder <alessandrofelder@users.noreply.github.com>
---
 docs/source/community/courses/index.md        |  9 +++++-
 .../materials/whole-brain-analysis/index.md   | 32 +++++++++++++++++++
 2 files changed, 40 insertions(+), 1 deletion(-)
 create mode 100644 docs/source/community/courses/materials/whole-brain-analysis/index.md

diff --git a/docs/source/community/courses/index.md b/docs/source/community/courses/index.md
index 47eed24f..d684096e 100644
--- a/docs/source/community/courses/index.md
+++ b/docs/source/community/courses/index.md
@@ -1,7 +1,14 @@
 # Courses
 
-Details of BrainGlobe training courses
+Details of BrainGlobe training courses:
 
+## Course materials
+```{toctree}
+:maxdepth: 1
+
+materials/whole-brain-analysis/index
+```
+## Previous courses
 ```{toctree}
 :maxdepth: 1
 
diff --git a/docs/source/community/courses/materials/whole-brain-analysis/index.md b/docs/source/community/courses/materials/whole-brain-analysis/index.md
new file mode 100644
index 00000000..835106e2
--- /dev/null
+++ b/docs/source/community/courses/materials/whole-brain-analysis/index.md
@@ -0,0 +1,32 @@
+# Whole brain microscopy analysis with BrainGlobe and napari
+
+This is designed as an in-person one-day course. However, our aim is that the materials can be referred to after the 
+course, and can be used for self-paced learning. 
+
+## Suggested schedule
+
+### Introduction
+* Installing BrainGlobe (30 mins)
+* Introduction to Image analysis with napari (45 mins)
+* Introduction to BrainGlobe (30 mins)
+
+### Tutorials
+* [Registering whole brain microscopy images with brainreg](/tutorials/tutorial-whole-brain-registration) (30 mins)
+* Segmenting structures in whole brain microscopy images with brainglobe-segmentation (30 mins)
+  * [1D structures](/tutorials/segmenting-1d-tracks)
+  * [2D/3D structures](/tutorials/segmenting-3d-structures)
+* Detecting cells in large 3D images with cellfinder (90 mins)
+  * [running cell detection](/tutorials/cellfinder-detection)
+  * [retraining your model](/tutorials/cellfinder-retraining)
+* [Analysing cell positions in atlas space](/tutorials/transform-cells-atlas) (30 mins)
+* Visualisation of data in atlas space (30 mins)
+  * [with brainrender-napari](/tutorials/visualise-atlas-napari) 
+  * [with brainrender](https://github.com/brainglobe/brainrender/tree/main/examples)
+
+### Wrap-up
+* Tour of other BrainGlobe tools (15 mins)
+* Feedback (5 mins)
+
+## Materials
+* [Slides](https://brainglobe.info/course-whole-brain-microscopy-analysis)
+* [GitHub repository](https://github.com/brainglobe/course-whole-brain-microscopy-analysis)
\ No newline at end of file