visualize ❭ cell_morphology_visualizer ❭ CellMorphologyVisualizer ❭ animation

CellMorphologyVisualizer.animation

visualize.cell_morphology_visualizer.CellMorphologyVisualizer.animation(images_path, overwrite_frames=False, color='grey', show_synapses=False, show_legend=False, client=None, t_start=None, t_stop=None, t_step=None, highlight_section=None, highlight_x=None, display=True, tpf=20)

Show an animation of the simulated neuron.

Creates a set of images of a neuron color-coded with voltage together with synapse activations. These images are then put together into a IPython animation using visualize.utils.display_animation_from_images The parameters :paramref:t_start, :paramref:t_stop and :paramref:t_step update the :paramref:self.time attribute

Parameters:

  • images_path (str) – path where the images for the gif will be generated.

  • overwrite_frames (bool) – whether to overwrite previously existing frames in the images_path directory.

  • color (str) – color of the cell morphology. Can be a fixed color, or a keyword referring to scalar data of the simulation, such as membrane voltage or ion channel dynamics.

  • show_synapses (bool) – whether to show the synapse activation locations onto the morphology.

  • show_legend (bool) – whether to show the color legend in the plot.

  • t_start (float) – start time point of our time series visualization

  • t_stop (float) – last time point of our time series visualization

  • t_step (float) – time between the different time points of our visualization_start (): start time point of our time series visualization

  • client (distrubted.client.Client) – dask client for parallelization

  • highlight_section (int) – section number of the section that should be highlighted with an arrow.

  • highlight_x (float) – x coordinate of the section that should be highlighted with an arrow.

  • display (bool) – whether to display the animation in the notebook.

  • tpf – time per frame (in ms)