Tutorials#

Getting started#

Atlas visualisation

Visualise atlas data in napari

Visualise an atlas in napari
3D registration

Registering a whole-brain dataset to an atlas.

Registering a whole-brain image to an atlas
Track segmentation

Manually segmenting a 1d track.

Segmenting a 1D track
Structure segmentation

Manually segmenting a 3d structure

Segmenting 2/3D structures
3D cell detection

Detecting cells in 3D with cellfinder in napari

Detecting cells in 3D with cellfinder
Analysing cell distributions

Analysing cell distributions in the brain with napari

Analysing brainwide distribution of cells
Retraining cellfinder

Retraining the cellfinder cell classification network in napari

Retraining the cellfinder classification network
Atlas download

Download an atlas with napari

Download an atlas through napari

Specific applications#

Probe segmentation

Analysis of silicon probe tracks (e.g. Neuropixels)

Silicon probe tracking
Bulk tracing analysis

Analyze and visualize bulk fluorescence tracing data

Analyze and visualize bulk fluorescence tracing data
Cell detection via brainmapper

Whole brain cell detection and registration

Whole brain cell detection and registration with the brainmapper command line tool
Exploring atlas data

Deepening understanding of atlas data and metadata (experimental!)

../aws_examples/explore_atlas.html

API tutorials#

BrainGlobe Atlas API

Using the BrainGlobe Atlas API to fetch and inspect an atlas

../api_examples/brainglobe_atlasapi.html

Template building (experimental)#

Preparing template inputs

Standardising and preprocessing images for template building (experimental!)

How to prepare input images for template building
Run template building

Configuring and running an HPC job for template building (experimental!)

Configuring a template-building run on the HPC
Aligning samples

Aligning samples to image axes for template building (experimental!)

Aligning samples for template building

Downloads#