From d6e66ac3c0355327cb0f67b0a9761faf962740b3 Mon Sep 17 00:00:00 2001
From: Adam Tyson <code@adamltyson.com>
Date: Mon, 22 Jul 2024 16:10:54 +0100
Subject: [PATCH] Add basic whole brain microscopy analysis course

---
 docs/source/community/courses/index.md        | 11 ++++++++--
 .../materials/whole-brain-analysis/index.md   | 21 +++++++++++++++++++
 .../courses/{ => scheduled}/dec-2023/index.md |  0
 3 files changed, 30 insertions(+), 2 deletions(-)
 create mode 100644 docs/source/community/courses/materials/whole-brain-analysis/index.md
 rename docs/source/community/courses/{ => scheduled}/dec-2023/index.md (100%)

diff --git a/docs/source/community/courses/index.md b/docs/source/community/courses/index.md
index a24b22d7..f3cbaba6 100644
--- a/docs/source/community/courses/index.md
+++ b/docs/source/community/courses/index.md
@@ -1,9 +1,16 @@
 # Courses
 
-Details of BrainGlobe training courses
+Details of BrainGlobe training courses:
 
+## Course materials
 ```{toctree}
 :maxdepth: 1
 
-dec-2023/index
+materials/whole-brain-analysis/index
+```
+## Scheduled courses
+```{toctree}
+:maxdepth: 1
+
+scheduled/dec-2023/index
 ```
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..d4348ea0
--- /dev/null
+++ b/docs/source/community/courses/materials/whole-brain-analysis/index.md
@@ -0,0 +1,21 @@
+# 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. 
+
+## Schedule
+### Introduction to BrainGlobe (30 mins)
+
+### Installing BrainGlobe (30 mins)
+
+### Registering whole brain microscopy images with brainreg (30 mins)
+
+### Segmenting structures in whole brain microscopy images with brainglobe-segmentation (30 mins)
+
+### Detecting cells in large 3D images with cellfinder (90 mins)
+
+### Analysing cell positions in atlas space (30 mins)
+
+### Visualisation of data in atlas space with brainrender and brainrender-napari (30 mins)
+
+### Tour of other BrainGlobe tools and wrap-up (30 mins)
\ No newline at end of file
diff --git a/docs/source/community/courses/dec-2023/index.md b/docs/source/community/courses/scheduled/dec-2023/index.md
similarity index 100%
rename from docs/source/community/courses/dec-2023/index.md
rename to docs/source/community/courses/scheduled/dec-2023/index.md