CellMorphologyInteractiveVisualizer¶

class visualize.cell_morphology_visualizer.CellMorphologyInteractiveVisualizer(cell, align_trunk=True, dash_ip=None, show=True, renderer='notebook_connected', t_start=None, t_stop=None, t_step=None)¶

Plot an interactive 3D render of a cell morphology using Plotly and Dash.

Initializes the CellMorphologyInteractiveVisualizer object.

Parameters:¶

cell : Cell¶

Cell object

align_trunk : bool¶

Whether or not to align the cell trunk with the z-axis.

dash_ip : str¶

IP address to run dash server on.

show : bool¶

set to False for testing

renderer : str¶

Type of backend renderer to use for rendering the javascript/HTML VBox. Defaults to “notebook_connected”

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

Attributes:¶

dash_ip¶

IP address to run dash server on.

Type:¶

str

show¶

Whether to show the plot. Set to False for testing purposes. Default: True

Type:¶

bool

background_color¶

Background color of the plot. Defaults to “#f0f0f0”

Type:¶

str

renderer¶

Type of backend renderer to use for rendering the javascript/HTML VBox. Defaults to “notebook_connected”. Available renderers are:

• ‘plotly_mimetype’

• ‘jupyterlab’

• ‘nteract’

• ‘vscode’

• ‘notebook’

• ‘notebook_connected’

• ‘kaggle’

• ‘azure’

• ‘colab’

• ‘cocalc’

• ‘databricks’

• ‘json’

• ‘png’

• ‘jpeg’

• ‘jpg’

• ‘svg’

• ‘pdf’

• ‘browser’

• ‘firefox’

• ‘chrome’

• ‘chromium’

• ‘iframe’

• ‘iframe_connected’

• ‘sphinx_gallery’

• ‘sphinx_gallery_png’

Type:¶

str

Methods:¶

_get_interactive_cell(color, time_point, diameter)	Setup plotly for rendering in notebooks.
_get_interactive_dash_app(color, t_start, t_stop, t_step)	This is the main function to set up an interactive plot with scalar data overlayed.
interactive_plot(color, renderer, diameter, time_point, show)	This method shows a plot with an interactive cell, overlayed with scalar data (if provided with the data argument).
interactive_app(color, t_start, t_stop, t_step)	param color: If you want some other color overlayed on the cell morphology.