EpiTools

epitools

EpiTools Plugin

    Workflow step:
    Image segmentationCell segmentation

    Licence PyPI Python Version tests Documentation coverage napari hub

    EpiTools is a Python package and associated napari plugin to extract the membrane signal from epithelial tissues and analyze it with the aid of computer vision.

    The development of EpiTools was inspired by the challenges in analyzing time-lapses of growing Drosophila imaginal discs.

    The folded morphology, the very small apical cell surfaces and the long time series required a new automated cell recognition to accurately study growth dynamics.

    Installation

    First, install napari.

    The recommended way to install EpiTools is via pip

    python -m pip install epitools

    To install the latest development version of EpiTools clone this repository and run

    python -m pip install -e .

    If working on Apple Silicon make sure to also install the following package from conda-forge.

    conda install -c conda-forge pyqt

    To also install the recommended plugins for the EpiTools workflow run

    python -m pip install epitools[wf]

    and

    python -m pip install -e .[wf]

    If working on Apple Silicon make sure to also install the following package from conda-forge

    conda install -c conda-forge cvxopt

    which is required for btrack.

    Issues

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

    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.

    Version:

    • 0.0.10

    Last updated:

    • 25 May 2023

    First released:

    • 04 May 2023

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    Open extension:

    Save extension:

    Save layers:

    GitHub activity:

    • Stars: 1
    • Forks: 0
    • Issues + PRs: 9

    Python versions supported:

    Operating system:

    Requirements:

    • PartSeg
    • magicgui
    • matplotlib
    • napari
    • numpy
    • pandas
    • scikit-image (>=0.20)
    • scipy

    Sign up to receive updates