devbio-napari

A bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.


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    A bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.

    PluginExplorationProcessingSegmentationMeasurementsClassificationVisualizationOther

    3d-ortho-viewer

    x

    accelerated-pixel-and-object-classification

    x x

    animation

    x

    blob-detection

    x

    brightness-contrast

    x

    cellpose

    x

    clusters-plotter

    xx

    crop

    x

    curtain

    x

    czifile2

    Read CZI files

    folder-browser

    x

    layer-details-display

    x List layer details

    mouse-controls

    x Pan through stacks, zoom by dragging

    PlatyMatch

    Registration

    plot-profile

    x

    plugin-search

    Search plugins

    process-points-and-surfaces

    xxx x

    pyclesperanto-assistant

    xxx

    RedLionfish

    x

    segment-blobs-and-things-with-membranes

    xx

    simpleitk-image-processing

    xxx

    skimage-regionprops

    x

    tabu

    x Handle multiple napari windows

    the-segmentation-game

    x

    workflow-inspector

    x Visualize workflows

    workflow-optimizer

    x Optimize image processing parameters

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

    Installation

    You can install devbio-napari via conda. If you have never used conda before, please read this guide first.

    conda create --name devbio-napari-env python=3.9 devbio-napari -c conda-forge
    conda activate devbio-napari-env

    Mac-users please also install this:

    conda install -c conda-forge ocl_icd_wrapper_apple

    Linux users please also install this:

    conda install -c conda-forge ocl-icd-system

    Afterwards, run this command from the command line

    naparia

    This window should open. It shows the Assistant graphical user interface. Read more about how to use it in its documentation.

    img.png

    Troubleshooting: Graphics cards drivers

    In case error messages contains "ImportError: DLL load failed while importing cl: The specified procedure could not be found" see also or ""clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR", please install recent drivers for your graphics card and/or OpenCL device. Select the right driver source depending on your hardware from this list:

    In case installation didn't work in the first attempt, you may have to call this command line to reset the napari configuration:

    napari --reset

    Contributing

    Contributions are very welcome. If you want to suggest a new napari plugin to become part of this distribution, please make sure it interoperates nicely with the other plugins. For example, if the plugin you suggest provided cell segmentation algorithms, please check if the resulting segmented cells can be analysed using napari-skimage-regionprops. Furthermore, please make sure the README of the plugin you are proposing comes with user documentation, e.g. a step-by-step guide with screenshots explaining what users can do with the plugin and how to use it. It is recommended to provide example data as well so that end-users can try out the plugin under conditions it was developed for.

    License

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

    Issues

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

    Version:

    • 0.5.9

    Release date:

    • 10 July 2022

    First released:

    • 08 June 2021

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 17
    • Forks: 4
    • Issues + PRs: 3

    Python versions supported:

    Operating system:

    Requirements:

    • napari-plugin-engine (>=0.1.4)
    • numpy (>=1.21.4)
    • napari-pyclesperanto-assistant
    • napari-skimage-regionprops
    • napari-animation
    • PlatyMatch
    • napari-plot-profile
    • napari-accelerated-pixel-and-object-classification
    • napari-brightness-contrast
    • napari-plugin-search
    • napari-segment-blobs-and-things-with-membranes
    • napari-simpleitk-image-processing
    • napari-folder-browser
    • napari-crop
    • napari-clusters-plotter
    • napari-tabu
    • redlionfish
    • napari-workflow-optimizer
    • napari-workflow-inspector
    • napari-curtain
    • napari-3d-ortho-viewer
    • cellpose-napari
    • napari-layer-details-display
    • napari (<=0.4.15)
    • vispy (<=0.9.6)
    • napari-mouse-controls
    • the-segmentation-game
    • napari-process-points-and-surfaces
    • napari-blob-detection
    • jupyterlab
    • napari-czifile2

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