Example gallery

These examples are small code snippets meant to illustrate certain pymaid functions. As per usual: have a look at the API reference to find out details about a given function.

Check this out

Pymaid is built on top of navis and navis functions can be used with CatmaidNeurons and CatmaidNeuronLists. Please check out the navis tutorials.

CatmaidNeuron/Lists

• Overview
• Indexing NeuronLists
• Parsing skeleton IDs

Visualization

• Plotting
  • 2D Plotting
  • Interactive 3D Plotting
• EM image data
  • Loading images
  • Plotting images
  • Load & save images

Morphology

• Morphological analyses
  • Basic properties
  • Rerooting, resampling, simplifying
  • Cutting, pruning, pasting

Connectivity

• Basics
• Compartmentalizing

CATMAID

• Fetching data
  • A quick primer
  • Fetching neurons
  • Fetching volumes
  • Obscure functions
  • Scaling things up
• Pushing data
  • Another quick primer
  • Annotations
  • Importing neurons

Interfaces

• Cytoscape

Misc

• URLs & random sampling
• User contributions
• Data caching
• Troubleshooting