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        "author": "Bj\u00f6rn Harink",
        "author_email": "bjorn@harink.info",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "MRBLEs Analysis Package\r\n=======================\r\nThis project aims to provide a package to **find**, **decode**, **extract**,\r\n**analyze** and MRBLEs using a set of images.\r\n\r\nThis package provides the tools to: (1) **find** the MRBLEs in a monochrome\r\nbrightfield microscopy image; (2) **decode** the MRBLEs beads by spectral\r\nunmxing, using reference spectra, and then spectrally decode the found beads\r\nusing Iterative Closest Point Matching and Gaussian Mixture Modeling; (3)\r\n**extract**, statistical values of interest in additional fluorescence\r\nchannels using the morphology of the MRBLEs, their locations, and respective\r\ncode; (4) **analyze** affinity information based on titrations of MRBLEs\r\nassays.\r\n\r\nMRBLEs project\r\n--------------\r\nMRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding) rely on\r\nspectral multiplexing to track analytes throughout an experiment. In these\r\nassays, we can create microspheres containing > 1,000 unique ratios of\r\nlanthanide nanophosphors that can be uniquely identified via imaging alone.\r\nWe are currently developing new assays that use these microspheres to\r\nunderstand how signaling proteins recognize their peptide substrates and to\r\nimprove our ability to extract information from single cells.\r\n\r\nAbstact on MRBLEs and the *mrbles* package\r\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\r\nMultiplexed bioassays, in which multiple analytes of interest are probed in parallel within a single small volume, have greatly accelerated the pace of biological discovery. Bead-based multiplexed bioassays have many technical advantages, including near solution-phase kinetics, small sample volume requirements, many within-assay replicates to reduce measurement error, and, for some bead materials, the ability to synthesize analytes directly on beads via solid-phase synthesis. To allow bead-based multiplexing, analytes can be synthesized on spectrally encoded beads with a 1:1 linkage between analyte identity and embedded codes. Bead-bound analyte libraries can then be pooled and incubated with a fluorescently-labeled macromolecule of interest, allowing downstream quantification of interactions between the macromolecule and all analytes simultaneously via imaging alone. Extracting quantitative binding data from these images poses several computational image processing challenges, requiring the ability to identify all beads in each image, quantify bound fluorescent material associated with each bead, and determine their embedded spectral code to reveal analyte identities. Here, we present a novel open-source Python software package (the mrbles analysis package) that provides the necessary tools to: (1) find encoded beads in a bright-field microscopy image; (2) quantify bound fluorescent material associated with bead perimeters; (3) identify embedded ratiometric spectral codes within beads; and (4) return data aggregated by embedded code and for each individual bead. We demonstrate the utility of this package by applying it towards analyzing data generated via multiplexed measurement of calcineurin protein binding to MRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding) containing known and mutant binding peptide motifs. We anticipate that this flexible package should be applicable to a wide variety of assays, including simple bead or droplet finding analysis, quantification of binding to non-encoded beads, and analysis of multiplexed assays that use ratiometric, spectrally encoded beads.\r\n\r\nLinks\r\n~~~~~\r\nPublication: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203725\r\n\r\nDocumentation: https://fordycelab.github.io/MRBLEs/\r\n\r\nSource code: https://github.com/FordyceLab/MRBLEs/\r\n\r\nInstallation\r\n------------\r\nThe MRBLEs software package is a Python Package available through the Python Package Index (PyPI): https://pypi.org/.\r\nTo makes us of ``mrbles`` follow the following instructions.\r\n\r\nPython installation\r\n~~~~~~~~~~~~~~~~~~~\r\nInstall (preferably) Python >3.5 Windows (https://www.python.org/downloads/windows/) or MacOS\r\n(https://www.python.org/downloads/mac-osx/). ``mrbles`` is built to be compatible with Pyhton >2.7,\r\nbut its dependencies (other Python Packages) are getting less and less support for Python 2.7.\r\n\r\nWindows\r\n_______\r\nThis is based on the detailed Windows installation instructions from the official Python page:\r\nhttps://docs.python.org/3/using/windows.html\r\n\r\n* Install Python by downloading the latest version of Python: https://www.python.org/downloads/.\r\n* Execute the installation file and follow the instructions.\r\n* On the first window make sure to tick the box \"*Add Pyhton x.x to PATH*\".\r\n* Preferably, use the \"*Customize installation*\".\r\n* On the second window use the standard selections, or if other people are using the same machine, also select \"*Install for all users*\".\r\n* Preferably, use a custumized installation location, e.g. for Python 3.7 \"C:\\Pyhton37\". This way it is easy to access when necessary.\r\n* Press \"*Install*\".\r\n\r\nTo make use of Python packages that do not come with a pre-compiled file (which `mrbles` does), as in they need to be\r\ncompiled on your computer from the source code. It is required to install a C++ compiler.\r\n\r\n* If using Python 2.7, install Microsoft Visual C++ Compiler for Python 2.7: https://www.microsoft.com/en-us/download/details.aspx?id=44266.\r\n* If using Python >3.6, install Build Tools for Visual Studio 2017: https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2017.\r\n* More info on compilers here: https://wiki.python.org/moin/WindowsCompilers#Which_Microsoft_Visual_C.2B-.2B-_compiler_to_use_with_a_specific_Python_version_.3F.\r\n\r\nMac OSx\r\n_______\r\nThis is based on the detailed Mac OSx installation instructions from the Python-Guide page: https://docs.python-guide.org/starting/install3/osx/#install3-osx\r\n\r\nThe installation for Mac OSx is slightly more complicated, but will help you in the future with Python dependencies.\r\n\r\n* First, download and install XCode: https://developer.apple.com/xcode/.\r\n\r\n - This is required for the installation of Python packages (C++ compiler) and for the installation of Brew, which is software that makes installing Python and dependencies much easier.\r\n\r\n* Second, install brew using the following command in Mac OSx Terminal:\r\n\r\n  ``ruby -e \"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)``\r\n\r\n\r\nThe ``mrbles`` package installation\r\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\r\nOnce Python is installed it can be accessed using your systems' Command Prompt (Windows) or Terminal (Mac OSx), using: ``python`` (if both Python 2 & 3 are installed this is: ``python3`` or ``python3``).\r\n\r\nTo install packages one can use the following commands, using the package name:\r\n\r\n* ``pip install package_name`` or\r\n\r\n* ``python -m pip install package_name``\r\n\r\nVisit the Python Package Index (PyPI) for package names: https://pypi.org/.\r\n\r\nNow that everything is installed the ``mrbles`` package can be installed, using the following commands in the terminal:\r\n\r\n* ``pip install mrbles`` (if both Python 2 & 3 are installed this is: ``pip3`` or ``pip``) or\r\n\r\n* ``python -m pip install mrbles`` (if both Python 2 & 3 are installed this is: ``pip3`` or ``pip``)\r\n\r\n\r\nUsing the ``mrbles`` package\r\n----------------------------\r\nThe ``mrbles`` package automatically installs the Jupyter Notebook environment: https://http://jupyter.org/.\r\n\r\nTo test the ``mrbles`` package download the example Notebook and all the data, reference, library (.xlsx), and flat-field files:\r\n\r\n* Notebook: https://github.com/FordyceLab/MRBLEs/blob/master/examples/example-notebook-GitHub-data.ipynb.\r\n* Data files: https://github.com/FordyceLab/MRBLEs/tree/master/data.\r\n\r\n - The quickest way is to download all the GitHub files in a zip file: https://github.com/FordyceLab/MRBLEs/archive/master.zip.\r\n\r\nThe set used for the publication can be found on a OSF repository. 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