Route:
Problems

P3 · Visualisation

Show these neurons together in a common template

Load skeletons/meshes with navis (+ pymaid/neuPrint loaders), plot co-registered.

Key question: Show these neurons together in a common template.

Route A: Python API

Load skeletons with navis and plot them co-registered in a common template space.

import navis
from vfb_connect import vfb

# Get neuron skeletons
neurons = vfb.get_skeletons(["VFB_jrchjtdb", "VFB_fw035286"])

# Plot in 3D
navis.plot3d(neurons, color=['red', 'blue'])

Route B: MCP Tool

Request 3D visualisation through the MCP tool.

Example Prompt

Show me the 3D image of neuron VFB_jrchjtdb and two of its strongest partners in the same template.

Route C: VFB Chat

Chat can help you find neurons to visualise, though for publication-quality figures you’ll want the Python API.

Optimized prompt: Ask for the image link and key morphology facts.

VFB Chat
Open in new tab

Tip: End your questions with "and give me the VFB IDs" to get identifiers you can use in Python.

Route D: 3D Circuit Browser

The Circuit Browser provides interactive 3D visualization with no code.
Open in Circuit Browser

When to Reach for Which Route

  • API/navis for publication figures and morphometric measurements
  • MCP/Chat for a quick look and orientation
  • 3D Browser for interactive exploration without code