Visualization

Tools for visualizing experimental data.

pyneurotrace.viz.plotIntensity(data, hz, branches=None, colors=None, stim=None, title=None, overlayStim=False, savePath=None, hybridStimColours=False, forceStimWidth=None, **kwargs)

Plots intensity data with optional branches and stimulus.

Parameters:

  • data (array) – Data to be plotted.

  • hz (int) – Sampling rate in Hz.

  • branches (array, optional) – Array of branch data. Default is None.

  • colors (array, optional) – Colors for the branches. Default is None.

  • stim (array, optional) – Array of stimulus data. Default is None.

  • title (str, optional) – Title for the plot. Default is None.

  • overlayStim (bool, optional) – Flag to overlay stimulus data. Default is False.

  • savePath (str, optional) – Path to save the plot. Default is None.

  • hybridStimColours (bool, optional) – Flag for hybrid stimulus colors. Default is False.

  • forceStimWidth (int, optional) – Force width for the stimulus. Default is None.

  • **kwargs (Additional keyword arguments for customization.)

Returns:

  • xAx (object) – x-axis object.

  • yAx (object) – y-axis object.

pyneurotrace.viz.plotLine(data, hz, branches=None, stim=None, labels=None, colors=None, title=None, yTitle='DF/F0', split=True, limitSec=None, overlayStim=True, savePath=None, hybridStimColours=True, yTickScale=1, yTickPct=True, yPad=0.05)

Plots line data with optional branches and stimulus.

Parameters:

  • data (array) – Data to be plotted.

  • hz (int) – Sampling rate in Hz.

  • branches (array, optional) – Array of branch data. Default is None.

  • stim (array, optional) – Array of stimulus data. Default is None.

  • labels (list, optional) – Labels for the lines. Default is None.

  • colors (array, optional) – Colors for the lines. Default is None.

  • title (str, optional) – Title for the plot. Default is None.

  • yTitle (str, optional) – Title for the y-axis. Default is ‘DF/F0’.

  • split (bool, optional) – Flag to split the lines. Default is True.

  • limitSec (tuple, optional) – Time limits for the plot in seconds. Default is None.

  • overlayStim (bool, optional) – Flag to overlay stimulus data. Default is True.

  • savePath (str, optional) – Path to save the plot. Default is None.

  • hybridStimColours (bool, optional) – Flag for hybrid stimulus colors. Default is True.

  • yTickScale (int, optional) – Scale for the y-axis ticks. Default is 1.

  • yTickPct (bool, optional) – Flag to format y-axis ticks as percentages. Default is True.

  • yPad (float, optional) – Padding for the y-axis. Default is .05.

Returns:

  • xAx (object) – x-axis object.

  • yAx (object) – y-axis object.

pyneurotrace.viz.plotAveragePostStimIntensity(data, hz, stimOffIdx, stimOnIdx, branches=None, title=None, secBefore=0, secAfter=3, savePath=None, **kwargs)

Plots average post-stimulus intensity.

Parameters:

  • data (array) – Data to be plotted.

  • hz (int) – Sampling rate in Hz.

  • stimOffIdx (int) – Index of stimulus off.

  • stimOnIdx (int, optional) – Index of stimulus on. Default is None.

  • branches (array, optional) – Array of branch data. Default is None.

  • title (str, optional) – Title for the plot. Default is None.

  • secBefore (int, optional) – Seconds before the stimulus. Default is 0.

  • secAfter (int, optional) – Seconds after the stimulus. Default is 3.

  • savePath (str, optional) – Path to save the plot. Default is None.

  • **kwargs (Additional keyword arguments for customization.)

Return type:

None

pyneurotrace.viz.plotAveragePostStimTransientParams(dfof, hz, stimOffsets, secAfter, vizTrace=None, savePath=None)

Plots average post-stimulus transient parameters.

Parameters:

  • dfof (array) – Data to be plotted.

  • hz (int) – Sampling rate in Hz.

  • stimOffsets (array) – Array of stimulus offsets.

  • secAfter (int) – Seconds after the stimulus.

  • vizTrace (int, optional) – Index of trace to visualize. Default is None.

  • savePath (str, optional) – Path to save the plot. Default is None.

Returns:

ax – Axis object.

Return type:

object

pyneurotrace.viz.plotPlanarStructure(tree, rootID, nodeXYZ, branchIDs=None, colors=None, title=None, flipY=False, scale=1, savePath=None, lineAlpha=0.8, flatten='Z', pixelMeters=None, palette='seaborn-v0_8-dark-palette', bgColor='black')

Plots a planar structure of the tree.

Parameters:

  • tree (dict) – Dictionary representing the tree structure.

  • rootID (int) – ID of the root node.

  • nodeXYZ (array) – Array of node locations (XYZ coordinates).

  • branchIDs (array, optional) – Array of branch IDs. Default is None.

  • colors (array, optional) – Colors for the branches. Default is None.

  • title (str, optional) – Title for the plot. Default is None.

  • flipY (bool, optional) – Flag to flip the y-axis. Default is False.

  • scale (float, optional) – Scale factor for the plot. Default is 1.

  • savePath (str, optional) – Path to save the plot. Default is None.

  • lineAlpha (float, optional) – Alpha value for the lines. Default is 0.8.

  • flatten (str, optional) – Axis to flatten. Default is ‘Z’.

  • pixelMeters (float, optional) – Pixel to meter conversion factor. Default is None.

  • palette (str, optional) – Color palette for the plot. Default is ‘seaborn-v0_8-dark-palette’.

  • bgColor (str, optional) – Background color for the plot. Default is ‘black’.

Returns:

ax – Axis object.

Return type:

object

pyneurotrace.viz.plotBaseTipScatter(baseTrace, tipTrace, title=None, **kwargs)

Scatter plot of all samples from traces from a filopodia tip vs. filopodia base.

Parameters:

  • baseTrace (array) – Base trace data.

  • tipTrace (array) – Tip trace data.

  • title (str, optional) – Title for the plot. Default is None.

  • **kwargs (Additional keyword arguments for customization.)

Returns:

ax – Axis object.

Return type:

object

pyneurotrace.viz.planarAnimation(tree, rootID, nodeXYZ, traceData, hz, flipY=False, stim=None, stimXY=(0, 0), radius=0.005, savePath=None, scale=1, flatten='Z')

Creates an animation of the planar structure with trace data.

Parameters:

  • tree (dict) – Dictionary representing the tree structure.

  • rootID (int) – ID of the root node.

  • nodeXYZ (array) – Array of node locations (XYZ coordinates).

  • traceData (array) – Array of trace data.

  • hz (int) – Sampling rate in Hz.

  • flipY (bool, optional) – Flag to flip the y-axis. Default is False.

  • stim (array, optional) – Array of stimulus data. Default is None.

  • stimXY (tuple, optional) – Stimulus position in the plot. Default is (0,0).

  • radius (float, optional) – Radius of the nodes. Default is 0.005.

  • savePath (str, optional) – Path to save the animation. Default is None.

  • scale (float, optional) – Scale factor for the plot. Default is 1.

  • flatten (str, optional) – Axis to flatten. Default is ‘Z’.

Returns:

anim – Animation object.

Return type:

object

pyneurotrace.viz.kymograph(kymoData, hz, smooth=False, title=None, widthInches=10, heightInches=60)

Shows raw intensity across the pixel line scanned around the POI to check for drift.

Parameters:

  • kymoData (array) – Kymograph data.

  • hz (int) – Sampling rate in Hz.

  • smooth (bool, optional) – Flag to smooth the data. Default is False.

  • title (str, optional) – Title for the plot. Default is None.

  • widthInches (int, optional) – Width of the plot in inches. Default is 10.

  • heightInches (int, optional) – Height of the plot in inches. Default is 60.

Returns:

ax – Axis object.

Return type:

object

pyneurotrace.viz.scrollingAnimation(data, hz, branches, stim, title, savePath)

Creates a scrolling animation of the data.

Parameters:

  • data (array) – Data to be animated.

  • hz (int) – Sampling rate in Hz.

  • branches (array) – Array of branch data.

  • stim (array) – Array of stimulus data.

  • title (str) – Title for the animation.

  • savePath (str) – Path to save the animation.

Returns:

anim – Animation object.

Return type:

object