Version:

  • 0.0.3

Release date:

  • 01 April 2022

First released:

  • 01 December 2021

License:

  • BSD-3-Clause

Supported data:

  • Information not submitted

GitHub activity:

  • Stars: 9
  • Forks: 2
  • Issues + PRs: 2

GitHub activity:

  • Stars: 9
  • Forks: 2
  • Issues + PRs: 2

Python versions supported:

  • >=3.8

Operating system:

  • OS Independent

Requirements:

  • Information not submitted

napari-time-series-plotter

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


    Authors:

    • Christopher Nauroth-Kress

    Authors:

    • Christopher Nauroth-Kress

    License Python Version PyPI Anaconda-Server Badge napari hub tests codecov

    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

    Demo gif

    • 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

    Version:

    • 0.0.3

    Release date:

    • 01 April 2022

    First released:

    • 01 December 2021

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 9
    • Forks: 2
    • Issues + PRs: 2

    Python versions supported:

    • >=3.8

    Operating system:

    • OS Independent

    Requirements:

    • Information not submitted

    Version:

    • 0.0.3

    Release date:

    • 01 April 2022

    First released:

    • 01 December 2021

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 9
    • Forks: 2
    • Issues + PRs: 2

    GitHub activity:

    • Stars: 9
    • Forks: 2
    • Issues + PRs: 2

    Python versions supported:

    • >=3.8

    Operating system:

    • OS Independent

    Requirements:

    • Information not submitted

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