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anatplot

anatplot is a Python package for plotting data on brain surfaces and visualizing anatomical regions in 3D. You can optionally add electrode contacts to any plot, then save a Matplotlib figure or explore and export the 3D scene.

Choose a plot

What you want to show Use Tutorial
A cortical map or parcel labels on brain surfaces SurfacePlot Surface basics
Selected regions from a labelled anatomical image ROIPlot ROI tutorial
A translucent whole-brain view that reveals contacts inside the brain VolumePlot Volume tutorial

Examples of SurfacePlot, ROIPlot, and VolumePlot

SurfacePlot has the most complete workflow, though its API may still evolve. ROIPlot and VolumePlot are under development.

Install

Install the current development release from PyPI with Python 3.10 or newer:

uv add "anatplot==0.1.0.dev0"

python -m pip install "anatplot==0.1.0.dev0"

Make your first figure

Draw a Neurosynth default-mode association map and a contact on inflated cortical surfaces.



import numpy as np

from anatplot import SurfacePlot, datasets

surfaces = datasets.fetch_surfaces("fsLR", surface="inflated", density="32k")
left, right = datasets.fetch_dmn_map_fslr32k()
association = {
    "left": np.ma.masked_equal(left, 0),
    "right": np.ma.masked_equal(right, 0),
}

# The with block automatically closes the scene and releases graphics resources.
with SurfacePlot(
    **surfaces,
    views=["lateral", "medial"],
    # Show left/right hemispheres side by side, with outer views above inner views.
    layout="grid",
    window_size=(1000, 600),
    zoom=1.5,
) as plot:
    plot.add_layer(association, cmap="YlOrRd", cbar=True, cbar_label="Association Z")
    plot.add_contacts([[-64, -13, 23]], radius=4, color="royalblue")
    fig = plot.to_figure(figsize=(10, 7))

fig.savefig("surface-map.png", dpi=300)
Cortical association map with one example contact

Acknowledgements