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 (30 mins)

• Segmenting structures in whole brain microscopy images with brainglobe-segmentation (30 mins)

  • 1D structures

  • 2D/3D structures

• Detecting cells in large 3D images with cellfinder (90 mins)

  • running cell detection

  • retraining your model

• Analysing cell positions in atlas space (30 mins)

• Visualisation of data in atlas space (30 mins)

  • with brainrender-napari

  • with brainrender

Wrap-up

• Tour of other BrainGlobe tools (15 mins)

• Feedback (5 mins)

Materials

• Slides

• GitHub repository