Usage

Start by importing neuroboom.

import neuroboom

Dendrograms

Dendrograms are 2D graph representation of 3D reconstructed neurons that preserve the local and global topology of the neuron.

The dendrogram functions within neuroboom recover treenode and connector information of a presented neuron and renders it as a NetworkX graph / network.

  • Treenodes are the nodes used to represent the neuron’s (skeletonised) morphology

  • Connectors are synapses (N.B. a single connector/synapse can have multiple connections)

As every connector (both presynaptic & postsynaptic) is associated with a specific treenode id (both on the presynaptic and postsynaptic neuron), dendrograms allows one to visualise which treenodes of a neuron are connected by specific neurons/ specific connectors.

This allows one to visualise the placement of synapses from specific neurons or lineage.

There are two options for dendrograms:

  1. Static

Static dendrograms are Matplotlib plots containing the 2D representation. These are best for scientific paper figures / presentations. ** See the dendrogram tutorial **

  1. Interactive

Interactive dendrograms use plotly to present the 2D representation. This allows for node / connector identification within the dendrogram. These are best for in progress analyses, however could also be used for scientific presentations.

For static dendrograms execute:

from neuroboom.dendrogram import plot_dendrogram

OR for interactive dendrograms:

from neuroboom.dendrogram import interactive_dendrogram