Tutorials#
Getting started#
Atlas visualisation
Visualise atlas data in napari
3D registration
Registering a whole-brain dataset to an atlas.
Track segmentation
Manually segmenting a 1d track.
Structure segmentation
Manually segmenting a 3d structure
3D cell detection
Detecting cells in 3D with cellfinder in napari
Analysing cell distributions
Analysing cell distributions in the brain with napari
Retraining cellfinder
Retraining the cellfinder cell classification network in napari
Atlas download
Download an atlas with napari
Specific applications#
Probe segmentation
Analysis of silicon probe tracks (e.g. Neuropixels)
Bulk tracing analysis
Analyze and visualize bulk fluorescence tracing data
Cell detection via brainmapper
Whole brain cell detection and registration
Aligning samples
Aligning samples to image axes for template building (experimental!)
Related tutorials#
These are tutorials hosted elsewhere that may be useful to BrainGlobe users.
Cell detection with BiaPy
Whole-brain microscopy analysis with BrainGlobe and BiaPy
