smo

Implementation of the Silver Mountain Operator (SMO) for the estimation of background distributions.


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    SMO is a Python package that implements the Silver Mountain Operator (SMO), which allows to recover an unbiased estimation of the background intensity distribution in a robust way.

    We provide an easy to use Python package and plugins for some of the major image processing softwares: napari, CellProfiler, and ImageJ / FIJI. See Plugins section below.

    Usage

    To obtain a background-corrected image, it is as straightforward as:

    import skimage.data
    from smo import SMO
    
    image = skimage.data.human_mitosis()
    smo = SMO(sigma=0, size=7, shape=(1024, 1024))
    background_corrected_image = smo.bg_corrected(image)

    where we used a sample image from scikit-image.

    A notebook explaining in more detail the meaning of the parameters and other possible uses for SMO is available here: smo/examples/usage.ipynb Open In Colab.

    Installation

    It can be installed with pip from PyPI:

    pip install smo

    Plugins

    Napari

    A napari plugin is available.

    To install:

    • Option 1: in napari, go to Plugins > Install/Uninstall Plugins... in the top menu, search for smo and click on the install button.

    • Option 2: just pip install this package in the napari environment.

    It will appear in the Plugins menu.

    CellProfiler

    A CellProfiler plugin in available in the smo/plugins/cellprofiler folder.

    To install, save this file into your CellProfiler plugins folder. You can find (or change) the location of your plugins directory in File > Preferences > CellProfiler plugins directory.

    ImageJ / FIJI

    An ImageJ / FIJI plugin is available in the smo/plugins/imagej folder.

    To install, download this file and:

    • Option 1: in the ImageJ main window, click on Plugins > Install... (Ctrl+Shift+M), which opens a file chooser dialog. Browse and select the downloaded file. It will prompt to restart ImageJ for changes to take effect.

    • Option 2: copy into your ImageJ plugins folder (File > Show Folder > Plugins).

    To use the plugin, type smo on the bottom right search box:

    select smo in the Quick Search window and click on the Run button.

    Note: the ImageJ plugin does not check that saturated pixels are properly excluded.

    Development

    Code style is enforced via pre-commit hooks. To set up a development environment, clone the repository, optionally create a virtual environment, install the [dev] extras and the pre-commit hooks:

    git clone https://github.com/maurosilber/SMO
    cd SMO
    conda create -n smo python pip numpy scipy
    pip install -e .[dev]
    pre-commit install

    How to cite this plugin

    If you use this plugin in your work, please cite it using the following citation. Don’t forget to cite napari too!

    Silberberg M., Grecco H.E. Robust and unbiased estimation of the background distribution for automated quantitative imaging DOI: 10.1101/2021.11.09.467975
    Download

    Version:

    • 2.0.0

    Release date:

    • 09 November 2021

    First released:

    • 21 September 2021

    License:

    • MIT

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 10
    • Forks: 3
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • numpy
    • scipy
    • typing-extensions ; python_version < "3.9"

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