From d6e66ac3c0355327cb0f67b0a9761faf962740b3 Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Mon, 22 Jul 2024 16:10:54 +0100 Subject: [PATCH 1/4] 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 From 5aaaed52c558c3e7614ce1894ba2637647f03920 Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Mon, 19 Aug 2024 11:10:25 +0100 Subject: [PATCH 2/4] Rename subsection --- docs/source/community/courses/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/community/courses/index.md b/docs/source/community/courses/index.md index f3cbaba6..0a19aba5 100644 --- a/docs/source/community/courses/index.md +++ b/docs/source/community/courses/index.md @@ -8,7 +8,7 @@ Details of BrainGlobe training courses: materials/whole-brain-analysis/index ``` -## Scheduled courses +## Previous courses ```{toctree} :maxdepth: 1 From 8e1f0d752ab07f1e4369d3d7717d6e9e18b2af3d Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Mon, 19 Aug 2024 14:42:17 +0100 Subject: [PATCH 3/4] Add links --- .../courses/materials/whole-brain-analysis/index.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/source/community/courses/materials/whole-brain-analysis/index.md b/docs/source/community/courses/materials/whole-brain-analysis/index.md index d4348ea0..83663477 100644 --- a/docs/source/community/courses/materials/whole-brain-analysis/index.md +++ b/docs/source/community/courses/materials/whole-brain-analysis/index.md @@ -18,4 +18,9 @@ course, and can be used for self-paced learning. ### 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 +### Tour of other BrainGlobe tools and wrap-up (30 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 From 114010f1c0edd58f99d9185a43b0be7dea682c12 Mon Sep 17 00:00:00 2001 From: alessandrofelder Date: Wed, 16 Oct 2024 16:48:05 +0100 Subject: [PATCH 4/4] beautify course schedule --- .../materials/whole-brain-analysis/index.md | 40 +++++++++++-------- 1 file changed, 23 insertions(+), 17 deletions(-) diff --git a/docs/source/community/courses/materials/whole-brain-analysis/index.md b/docs/source/community/courses/materials/whole-brain-analysis/index.md index 83663477..835106e2 100644 --- a/docs/source/community/courses/materials/whole-brain-analysis/index.md +++ b/docs/source/community/courses/materials/whole-brain-analysis/index.md @@ -3,23 +3,29 @@ 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) - +## 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)