Tutorials

These tutorials are meant to illustrate certain NAVis functions. As per usual: have a look at the API reference to find out details about a given function. There you will also find more examples.

The Basics

Working with navis neurons:

• Neuron types
• Lists of Neurons
• Neuron Math
• Comparing Neuron/Lists
• Making custom changes
• Converting neuron types
• Neuron attributes

Import/Export

Local data:

• Skeletons
• Meshes
• Voxel / Image Data
• Dotprops
• Pickling

Remote data sources & repositories:

• neuPrint
• MICrONS Datasets
• Neuroglancer & CloudVolume
• Neuromorpho
• Insect Brain DB

Plotting

Visualize your neurons

• Overview
• 2D plots
• 3D plots
• 1D plots
• Dendrograms & more
• Videos
• XKCD

Morphology

Morphometrics:

• Basic Properties
• Segment Analysis
• Sholl Analysis
• Geodesic Distances

Processing:

• Rerooting
• Simplifying
• Smoothing
• Cutting & Pruning
• Intersecting with Volumes

NBLAST

Run & interpret NBLAST:

• NBLAST
  • What is NBLAST?
  • Running NBLAST
  • Another flavour: syNBLAST
  • A real-world example
• NBLAST against FlyCircuit
• NBLAST using light-level data
• Custom score matrices

Interfaces

Use navis in combination with other tools:

• NEURON simulator
• Blender 3D
• R and the nat libraries

Transformations

Transform spatial data (e.g. neurons) between brain spaces:

• Transformations
  • Introduction
  • flybrains
  • Using xform_brain
  • Using mirror_brain
  • Low-level functions

Misc

• Multiprocessing
  • Running navis functions in parallel
  • Parallelizing generic functions
• Troubleshooting

Not seeing what you’re looking for? Need additional pointers? Found a broken example? Open an issue or use discussions on Github to ask questions!