Package: napari-time-series-plotter
napari-time_series_plotterDescriptionNapari-time_series_plotter (TSP) is a plugin for thenaparindimensional image viewer.TSPadds live plotting of time-resolved images to napari. You can select and visualize pixel/voxel or ROI mean values from one or multiple image layers as intensity-over-time line plots (The first image dimension is handled as time) and save the figures or the underlying time series data as CSV file. TSP supports 3D to nD images (3D: t+2D, nD: t+nD).Plottingis handeled by theExplorerwidget, it offers three different plotting modes: Voxel, Shapes, Points--> Voxel mode offers live plotting while moving the cursor over an image layer--> Shapes mode offers shape-based ROI plotting the ROI combination method can be one of [Mean, Median, STD, Sum, Min, Max]; multiple ROIs can be plotted simultaneously--> Points mode offers simultaneous, point-based plotting of multiple voxelsYou can modify and save the plots through the canvas toolbar.Plotting powered bynapari-matplotlib.Viewingthe time series as a table is handled by theInspectorwidget. You can load the data you've plotted and inspect the single time point values of each selection. The columns are named like the plots in theExplorer. You can copy the whole tabe or a selection to the clipboard or directly expot it to a CSV file to save the time series.InstallationYou can either install the latest version via pip or conda.pip:pip install napari-time-series-plotteror download the packagedtar.gzfile from the release assets and install it withpip install /path/to/file.tar.gzconda:conda install -c conda-forge napari-time-series-plotterAlternatively, you can install the plugin directly in thenapariviewer plugin manager, the napari hub, or the release assets.To install the latest development version install directly from the relevant GitHub branch.UsageBasics and Live plottingSelect theTSPExplorerwidget in thePluginstab of the napari viewerUse theLayerSelectorto choose the image layers you want to source for plottingMove the corsor over the layer while holding "Shift"TheOptionstab offers multiple options to customize your plot.Set custom title or axe labelsSwitch between autoscaling and manually defined max and min values of the axesSwitch to label truncation in the options tab if your layer names are too long for the figure legend (set max length manually)Set a scaling factor for the X-axisThe plot can be modified and saved through its toolbar above.Plotting ROIsSelect the Shapes plotting mode via theOptionstab (Voxel mode is the default).Use theLayerSelectorto choose the image layers you want to source for plotting.Add one ore more shapes to the "ROI Selection" layer.The "ROI Selection" shapes are 2D only, effecting the currently displayed slice.(newly added shapes might have to be moved before they are correctly plottet)Reposition or remove shapes if needed.Change the ROI mode in theOptionstab (Default: mean).Plotting multiple PointsSelect the Shapes plotting mode via theOptionstab (Voxel mode is the default).Use theLayerSelectorto choose the image layers you want to source for plotting.Add one or more points to the "Point selection" layer.The points can be on different slices (3D and 4D support only) or images (grid mode)Reposition or remove points if needed.View time series as tableSelect theTSPInspectorwidget in thePluginstab of the napari viewerPress the load from plot button to load the currently displayed plots into theInspectorYou can copy the whole table or a selection to your clipboard or export it to CSV file through the buttons above.ToDo (help welcome)Add Sphinx documentationVersion 0.1.0 MilestonesUpdate to napari-plugin-engine2#5Update widget GUI#6Add widget to save pixel/voxel time series to file#7Add ROI and multi-voxel plotting#14Evaluate and close remaining issues (#22,#25,)ContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-time_series_plotter" is free and open-source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.ReferencesThisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.Images used in the demo gif were taken fromThe Cancer Imaging ArchiveDOI: https://doi.org/10.7937/K9/TCIA.2015.VOSN3HN1
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