neuromaps_mouse.plotting.plot_allenccfv3_ortho

neuromaps_mouse.plotting.plot_allenccfv3_ortho(regions, values, section_coords=(6587.84, 3849.08, 5688.16), cmap='viridis', clim=None, cnorm=None, show_colorbar=True, cbar_title=None, equal_scale=True, equal_scale_zoom=1, show_scale=True, show_coord=True, figsize=(3, 1), cbar_kws=None, lc_kws=None, pc_kws=None, verbose=1)[source]

Plot Allen CCFv3 brain regions in three orthogonal views.

This function creates a 1x3 subplot figure displaying coronal, axial, and sagittal cross-sections of the Allen Common Coordinate Framework v3. Specified brain regions are colored according to provided values.

Parameters:

  • regions (array-like of str) – Brain region acronyms to plot (e.g., [‘VIS’, ‘SS’]).

  • values (array-like of float) – Data values for each region, used for colormap mapping.

  • section_coords (tuple of float, optional) – Coordinates (x, y, z) for the three planes in micrometers. Default is (6587.84, 3849.08, 5688.16).

  • cmap (str, optional) – Name of the colormap to use. Default is ‘viridis’.

  • clim (tuple of float, optional) – Colormap limits (vmin, vmax). If None, uses 2.5-97.5 percentiles of values. Default is None.

  • cnorm (matplotlib.colors.Normalize, optional) – Custom normalization for colormap. If None, created from clim. Default is None.

  • show_colorbar (bool, optional) – Whether to display a colorbar. Default is True.

  • cbar_title (str, optional) – Title label for the colorbar. Default is None.

  • equal_scale (bool, optional) – Whether to use equal scaling across all axes. Default is True.

  • equal_scale_zoom (float, optional) – Zoom factor for equal scaling (1 = full view). Default is 1.

  • show_scale (bool, optional) – Whether to display a scale bar. Default is True.

  • show_coord (bool, optional) – Whether to display section coordinates on each subplot. Default is True.

  • figsize (tuple of float, optional) – Figure size as (width, height) in inches. Default is (3, 1).

  • cbar_kws (dict, optional) – Additional keyword arguments for colorbar configuration. Default is None.

  • lc_kws (dict, optional) – Keyword arguments for LineCollection (e.g., color, lw). Default is None.

  • pc_kws (dict, optional) – Keyword arguments for PolyCollection. Default is None.

  • verbose (int, optional) – Verbosity level for warnings about unavailable regions. Default is 1.

Returns:

  • fig (matplotlib.figure.Figure) – The figure object containing the subplots.

  • axes (numpy.ndarray) – Array of matplotlib.axes.Axes objects (shape 3,).

Notes

Brain regions not found in the structure mesh database are excluded with an optional warning. The Allen CCFv3 reference brain mesh is fetched automatically on first call.

Examples

>>> regions = ['VIS', 'SS', 'MO']
>>> values = [0.5, 0.7, 0.3]
>>> fig, axes = plot_allenccfv3_ortho(regions, values, cbar_title='Signal')