iacs-ipac-reader

iacs-ipac-reader

A reader plugin for read iacs/ipac images and export .rtdc files.


    License PyPI Python Version tests codecov napari hub

    A plugin used a convolutional neural network (CNN) to distinguish single platelets, platelet clusters, and white blood cells and performed classical image analysis for each subpopulation individually. Based on the derived single-cell features for each population, a Random Forest (RF) model was trained and used to classify COVID-19 associated thrombosis and non-COVID-19 associated thrombosis.

    More information about IACS/iPAC.
    IACS: DOI: 10.1016/j.cell.2018.08.028
    iPAC: DOI: 10.7554/eLife.52938


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

    Installation

    You can install iacs_ipac_reader via pip:

    pip install iacs_ipac_reader

    To install latest development version :

    pip install git+https://github.com/zcqwh/iacs_ipac_reader.git

    Introduction

    The iacs-ipac-reader plugin mainly include 3 functional tabs:

    • iPAC
    • IACS
    • AID classif.

    iPAC image contour tracker

    Interface of iPAC contour tracker

    ipac.

    IACS image contour tracker

    Interface of IACS contour tracker

    iacs.

    AID classif.

    Interface of AID classif.

    AID_classif.

    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, "iacs_ipac_reader" is free and open source software

    Issues

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

    Version:

    • 0.0.13

    Release date:

    • 12 April 2022

    First released:

    • 21 January 2022

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 1
    • Forks: 0
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • h5py (>=3.5.0)
    • napari (>=0.4.12)
    • napari-plugin-engine (>=0.2.0)
    • numpy (>=1.21.4)
    • opencv-contrib-python-headless (>=4.4.0.46)
    • openpyxl (>=3.0.9)
    • sklearn (>=0.0)
    • PyQt5 (==5.12.3)
    • pandas (>=1.4.0)

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