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        "author": "Arve Seljebu",
        "author_email": "arve.seljebu@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: Implementation :: PyPy"
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        "description": "leicaexperiment\n===============\n\n|build-status-image| |pypi-version| |wheel|\n\nOverview\n--------\n\nThis is a python module for interfacing with *Leica LAS AF/X Matrix\nScreener* experiments.\n\nThe module can be used to:\n\n-  stitch wells from an experiment exported with the *LAS AF Data\n   Exporter*\n-  batch compress images lossless\n-  programmatically select slides/wells/fields/images given by\n   attributes like\n\n   -  slide (S)\n   -  well position (U, V)\n   -  field position (X, Y)\n   -  z-stack position (Z)\n   -  channel (C)\n\nFeatures\n--------\n\n-  Access experiment as a python object\n-  Compress to PNGs without loosing precision, metadata or colormap\n-  ImageJ stitching (Fiji is installed via\n   `fijibin <https://github.com/arve0/fijibin>`__)\n\nInstallation\n------------\n\nInstall using ``pip``...\n\n.. code:: bash\n\n    pip install leicaexperiment\n\nExamples\n--------\n\nstitch experiment\n^^^^^^^^^^^^^^^^^\n\n.. code:: python\n\n    from leicaexperiment import Experiment\n\n    # path should contain AditionalData and slide--S*\n    experiment = Experiment('path/to/experiment')\n\n    # if path is omitted, experiment path is used for output files\n    stitched_images = experiment.stitch('/path/to/output/files/')\n\n    # get information about placement of images in the stitch\n    xs, ys, attrs = experiment.stitch_coordinates(well_x=0, well_y=0)\n\nstitch specific well\n^^^^^^^^^^^^^^^^^^^^\n\n.. code:: python\n\n    from leicaexperiment import stitch\n\n    stitched_images = stitch('/path/to/well')\n\ndo stuff on all images\n^^^^^^^^^^^^^^^^^^^^^^\n\n.. code:: python\n\n    from leicaexperiment import Experiment\n\n    experiment = Experiment('path/to/experiment--')\n\n    for image in experiment.images:\n        do stuff...\n\ndo stuff on specific wells/fields\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n.. code:: python\n\n    from leicaexperiment import Experiment\n    from PIL import Image\n\n    experiment = Experiment('path/to/experiment--')\n\n    # on images in well --U00--V00\n    for well in experiment.well_images(0, 0):\n        do stuff...\n\n    # rotate top left image in first row\n    rows = experiment.well_rows\n    for r in rows:\n        img_path = experiment.image(r, 0, 0, 0)\n        img = Image.open(img_path)\n        img = img.rotate(90)\n        img.save(img_path)\n\nsubtract attributes from file names\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n.. code:: python\n\n    from leicaexperiment import attribute\n\n    # get all channels\n    channels = [attribute(image, 'C') for image in experiment.images]\n    min_ch, max_ch = min(channels), max(channels)\n\nbatch lossless compress of experiment\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n.. code:: python\n\n    from leicaexperiment import Experiment\n\n    e = Experiment('/path/to/experiment')\n    pngs = e.compress()\n    print(pngs)\n\nAPI reference\n-------------\n\nAPI reference is at http://leicaexperiment.rtfd.org.\n\nDevelopment\n-----------\n\nInstall dependencies and link development version of leicaexperiment to\npip:\n\n.. code:: bash\n\n    git clone https://github.com/arve0/leicaexperiment\n    cd leicaexperiment\n    pip install -r requirements.txt\n\nrun test\n^^^^^^^^\n\n.. code:: bash\n\n    pip install tox\n    tox\n\nextra output, jump into pdb upon error\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n.. code:: bash\n\n    DEBUG=leicaexperiment tox -- --pdb -s\n\nbuild api reference\n^^^^^^^^^^^^^^^^^^^\n\n.. code:: bash\n\n    pip install -r docs/requirements.txt\n    make docs\n\n.. |build-status-image| image:: https://secure.travis-ci.org/arve0/leicaexperiment.png?branch=master\n   :target: http://travis-ci.org/arve0/leicaexperiment?branch=master\n.. |pypi-version| image:: https://pypip.in/version/leicaexperiment/badge.svg\n   :target: https://pypi.python.org/pypi/leicaexperiment\n.. |wheel| image:: https://pypip.in/wheel/leicaexperiment/badge.svg\n   :target: https://pypi.python.org/pypi/leicaexperiment",
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