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Add whole brain microscopy analysis course (#221)
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Co-authored-by: alessandrofelder <[email protected]>
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adamltyson and alessandrofelder authored Oct 16, 2024
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9 changes: 8 additions & 1 deletion docs/source/community/courses/index.md
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# 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
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# 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)

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