CellMorphologyVisualizer.write_gif

visualize.cell_morphology_visualizer.CellMorphologyVisualizer.write_gif(images_path, out_name, 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, overwrite_frames=False, tpf=20)

Creates a set of images where a neuron morphology color-coded with voltage together with synapse activations are shown for a set of time points. In each image the neuron rotates a bit (3 degrees) over its axis. These images are then put together into a gif. The parameters t_start, t_stop and t_step will define the times_to_show attribute

Parameters:
images_path : str

dir where the images for the gif will be generated

out_name : str

path location of the resulting gif.

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.

client : distributed.client.Client

dask client for parallelization

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

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.

overwrite_frames : bool

whether to overwrite previously existing frames in the images_path directory.

tpf : float

duration of each frame in ms