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=20¶

time per frame (in ms)