Adaptive Pixel Reassignment

napari-ISM

It performs Adaptive Pixel Reassignment.


    napari hub License PyPI Python Version

    It performs Adaptive Pixel Reassignment via a phase-correlation algorithm. Once installed, you can upload any ISM-dataset in .h5 or .npy format. The plugin expects a numpy array of the format rzxytc (r: repetition, z: axial dimension, xy: lateral dimensions, t: time dimension, c: detector element). If the rzt dimensions are not present, add manually fake dimensions (e.g. using the numpy.expand_dims function). You can also generate a synthetic ISM-dataset from the File menu. Once a dataset is uploaded on an image layer, you can use the Napari plugin menu to perform either a sum on the c dimension or perform Adaptive Pixel Reassignment on the c dimension.


    Installation

    You can install napari-ISM via pip:

    pip install napari-ISM

    It requires the following Python packages

    numpy
    scipy
    scikit-image
    h5py
    napari

    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 GNU LGPL v3.0 license, "napari-ISM" is free and open source software

    Issues

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

    Version:

    • 0.1.0

    Release date:

    • 26 May 2022

    First released:

    • 26 May 2022

    License:

    • LGPL-3.0

    Supported data:

    • Information not submitted

    Open extension:

    Save extension:

    Save layers:

    GitHub activity:

    • Stars: 0
    • Forks: 0
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • numpy
    • scipy
    • scikit-image
    • h5py
    • napari
    • magicgui
    • qtpy

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