Plotting ToolsΒΆ

The scaffold package provides tools to plot network topology (either point and detailed networks) and morphologies in the bsb.plotting module.

To plot a network saved in a bsb instance, you can use:

  • plot_network_cache(scaffold): to plot the network saved in the memory cache after having compiled it

  • plot_network(scaffold): to plot a network, adding the keyword argument from_memory=False if you want to plot a network saved in a previously compiled HDF5 file. The default value is from_memory=True, which plots the version saved in your cache (you should have compiled the network in the current session).

  • plot_network_detailed(scaffold): Plots cells represented by their fully detailed morphologies. These plots are usually not able to render more than a 30-50 cells at the same time depending on the complexity of their morphology.

You can also plot morphologies:

  • plot_morphology(m): Plots a Morphology

  • plot_fiber_morphology(fm): Plots a FiberMorphology

  • plot_voxel_cloud(m.cloud): Plots a VoxelCloud

All of the above functions take a fig keyword argument of type plotly.graph_objects.Figure in case you want to modify the figure, or combine multiple plotting functions on the same figure, such as plotting a morphology and the voxel cloud of its axon.