Plotting and Visualization

Cedalion’s visualization modules cover three levels of output:

  • Time-domain plots (cedalion.vis.timeseries) — channel time traces, haemoglobin concentration time courses, and epoch butterfly plots for quality checking and results communication.

  • Scalp-level maps (cedalion.vis.anatomy) — project channel-space values onto a 2-D scalp topography or onto a 3-D scalp mesh. Includes sensitivity matrix visualisation for assessing channel coverage.

  • Quality summary (cedalion.vis.quality) — channel-by-channel quality dashboards showing SCI, SNR, and motion artefact flags.

Plots are built from composable building blocks in cedalion.vis.blocks (individual channel waveforms, quality colorbars, etc.) and cedalion.vis.colors (colormap utilities). For 3-D rendering Cedalion uses PyVista; 2-D plots use Matplotlib.

Two Qt-based interactive GUIs are available for manual inspection:

  • Time series inspector — cedalion.vis.misc.time_series_gui

  • Probe montage viewer — cedalion.vis.misc.plot_probe_gui

These subpackages contain building blocks to assemble visualizations:

cedalion.vis.blocks

Blocks of plotting functionality to build visualizations.

cedalion.vis.colors

Color and colormap definitions.

The functions in these subpackages create complete plots for different usage scenarios:

cedalion.vis.anatomy

Tools for visualizing data on brain and scalp surface representations.

cedalion.vis.anatomy.sensitivity_matrix

Plots an fNIRS probe's sensitivity profile on a 3D brain surface.

cedalion.vis.quality

Tools for visualizing signal quality metrics and masks.

cedalion.vis.timeseries

Tools for plotting temporal data.

Cedalion contains two Qt-based GUIs for inspecting time series and probes:

cedalion.vis.misc.plot_probe_gui

Interactive GUI to view the HRF in probe space after data has been processed.

cedalion.vis.misc.time_series_gui

Interactive GUI to plot fNIRS probe and channel time courses.

Examples

Visualization Examples using Cedalion Plot Functions