neuromaps_mouse.plotting.plot_allenccfv3_ortho_asym

neuromaps_mouse.plotting.plot_allenccfv3_ortho_asym(regions_lh, regions_rh, values_lh, values_rh, 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 with separate left/right hemisphere data.

This function creates a display showing three orthogonal views of the Allen CCF v3, with left and right hemisphere regions colored with potentially different values. This is useful for visualizing lateralized data or comparing hemispheric differences.

Parameters:

  • regions_lh (array-like of str) – Brain region acronyms for left hemisphere.

  • regions_rh (array-like of str) – Brain region acronyms for right hemisphere.

  • values_lh (array-like of float) – Data values for left hemisphere regions.

  • values_rh (array-like of float) – Data values for right hemisphere regions.

  • 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 combined left/right 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 displaying the combined orthogonal views.

  • ax (matplotlib.axes.Axes) – A single axes object displaying the composite image.

Notes

This function generates separate left and right hemisphere plots using plot_allenccfv3_ortho, then stitches them together into a single image with alternating left/right views. The stitching respects the z-coordinate of section_coords to determine which hemisphere to show in the axial view.

Examples

>>> regions_lh = ['VIS', 'SS']
>>> regions_rh = ['VIS', 'SS']
>>> values_lh = [0.5, 0.7]
>>> values_rh = [0.6, 0.8]
>>> fig, ax = plot_allenccfv3_ortho_asym(
...     regions_lh, regions_rh, values_lh, values_rh,
...     cbar_title='Asymmetry Index'
... )