napari-time-series-plotter

Description

Napari-time_series_plotter (TSP) is a plugin for the napari image viewer. TSP adds widgets to the viewer to select and visulise pixel / voxel values from one or multiple image layers as line plots. A plot represents the intensity of the selected pixel / voxel over the first dimension (time). TSP supports 3D and 4D images (4D: t+3D, 3D: t+2D).

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Installation

You can either install the latest version via pip or conda.

pip:

pip install napari-time-series-plotter

conda:

conda install -c conda-forge napari-time-series-plotter

Alternatively you can install the plugin directly in the napari viewer plugin manager.

To install the latest development version use:

pip install git+https://github.com/ch-n/napari-time_series_plotter.git

Usage

• Select the two TSP widgets LayerSelectror and VoxelPlotter in the Plugins tab in the viewer
• Use the LayerSelector to chose the image layers you want to select for plotting
• Move the mouse over the image while holding Shift
• The plotter will display graphs for all selected layers and a legend

ToDo

• Add Sphinx documentation

Version 0.1.0 Milstones

• Update to napari-plugin-engine2 #5
• Update widget GUI #6
• Add widget to save pixel / voxel time series to file #7

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-time_series_plotter" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

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References

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Images used in the demo gif were taken from: The Cancer Imaging Archive

DOI: https://doi.org/10.7937/K9/TCIA.2015.VOSN3HN1
Images: 1.3.6.1.4.1.9328.50.16.281868838636204210586871132130856898223
        1.3.6.1.4.1.9328.50.16.254461916058189583774506642993503110733