pymaid 2.4.0
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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

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Source

© Copyright 2017, Philipp Schlegel.
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