A Plugin for napari to visualize pixel values over the first dimension (time -> t+3D, t+2D) as graphs.
Project description
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).
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.
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
Project details
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