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        "author": "IOCBio team",
        "author_email": "iocbio@sysbio.ioc.ee",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: X11 Applications :: Qt",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering"
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        "description": "# Semi-automatic calcium sparks detection software\n\nIOCBIO Sparks is a cross-platform application for analysis and\ndetection of calcium sparks when imaged using confocal microscope line\nscanning mode. \n\nIOCBIO Sparks is a free software released under the GNU General Public\nLicense (GPL), see the file [`LICENSE`](LICENSE) for details. \n\nFor testing the software, we have uploaded example datasets at\nhttps://sysbio.ioc.ee/software/iocbio-sparks .\n\nResults of the analysis are stored in the database (schema described\nin [docs/database-schema](docs/database-schema) and, if needed, can be\nexported into spreadsheet file.\n\n## Citations and software description\n\nSoftware is described in a paper published in PeerJ (see below) that\ngives a background information regarding use of the software and shows\nan example analysis of sparks. Please cite this paper if you use the\nsoftware.\n\nLaasmaa, M., Karro, N., Birkedal, R., & Vendelin, M. (2019). IOCBIO\nSparks detection and analysis software. _PeerJ_, 7, e6652\nhttps://doi.org/10.7717/peerj.6652\n\n## Installation\n\nThere are several ways to install the software. The application\nrequires python3.\n\nFor Linux, at present, installation using `pip` is recommended. It is\nexpected that `pip` soulution would work for Mac as well. \n\nFor Windows, `conda` solution is recommended for users that don't have\nPython installed already. Otherwise, if using other than Anaconda\nPython, consider using `pip` solution.\n\n### pip\n\nTo be able to install PyQt5 using pip, you have to use python3.5 or\nhigher. If not available in the system, you can replace `pip3` command\nbelow with `python3 -m pip`.\n\nTo install published version, run\n\n```\npip3 install --user iocbio.sparks\n```\nThis will install all dependencies and it is expected to add a command `iocbio-sparks` into your `PATH`. \nIf the command is missing after installation, check whether the default location\nof `pip3` installation is in your path. For Linux, it should be `~/.local/bin`.\n\nIts possible to install from Git repository directly:\n```\npip3 install --user git+https://gitlab.com/iocbio/sparks\n```\n\nFor development, use\n\n```\npip3 install --user -e .\n```\n\nin the source directory. To install the current version from the source, use\n\n```\npip3 install --user .\n```\n\nNote that `--user` is recommended to avoid messing up the system\npackages.\n\n\n### conda (Anaconda or Miniconda3)\n\nHere, concise installation instructions are given. For illustrated\ninstructions with screenshots, see [Detailed Anaconda\ninstructions](docs/INSTALL.Anaconda.md)\n\n#### Installation Anaconda\n\nInstall Anaconda Python environment by downloading it from\nhttps://www.anaconda.com/ . The package uses Python 3 language, so,\nthe version supporting it should be installed. At the moment of\nwriting, its Python 3.6.\n\n#### Installation of iocbio.sparks\n\nFor installation from GUI:\n* Start Anaconda Navigator\n* Add channels by clicking \"Channels\" on the main screen and adding: \n    * conda-forge\n    * iocbio\n* icon for `iocbio.sparks` application should appear on the main\n  Anaconda Navigator. Click on its install for installation.\n  \nPlease note, it may take several minutes to install the application due \nto its dependencies. \n\nFor installation from CLI, start Anaconda Prompt. In the prompt, add channels:\n```\nconda config --append channels conda-forge\nconda config --append channels iocbio\n```\nand install software\n```\nconda install -c iocbio iocbio-sparks\n```\nand you are all set.\n\nFor running iocbio.sparks in Windows, its possible to start it as an\napplication from Anaconda Navigator or, directly, from starting\n`iocbio-sparks` in `Anaconda/Scripts` directory. For convinience, a\nshortcut can be created on desktop or Start Menu by the user.\n\n\n## Copyright\n\nCopyright (C) 2018 Laboratory of Systems Biology, Department of\nCybernetics, School of Science, Tallinn University of Technology.\n\nAuthors:\n* Martin Laasmaa\n* Marko Vendelin\n\nContact: Marko Vendelin <markov@sysbio.ioc.ee>\n\nSoftware license: the GNU General Public License as published by the\nFree Software Foundation, either version 3 of the License, or (at your\noption) any later version. See [`LICENSE`](LICENSE) for details\n\nFor any other licenses, please contact the authors.",
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