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        "description": "BioPrinter\n===========\n.. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/bioprinter.svg?branch=master\n   :target: https://travis-ci.org/Edinburgh-Genome-Foundry/bioprinter\n   :alt: Travis CI build status (Python 3)\n\nBioprinter (webpage here_ ) is a Python module to produce living art. It transforms an image into files that a liquid dispenser can use to *print* the image to a plate using pigmented yeast or bacteria.\n\nHere are two examples of bio-art:\n\n.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_dolly.jpeg\n    :align: center\n\n    Dolly drawn with baker yeast (white), violacein-producing yeast (black), and carotene-producing yeast (orange)\n\n\n.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_england.jpeg\n    :align: center\n\n    England flag drawn with 3 different strains of the bacterium *E. coli*.\n\nThese bio-prints (and many others!) were presented at the University of Edinburgh's SynthSys Open days 2016 (strain selection and acoustic printing by Paulina Kanigowska).\n\nBioprinter is released on Github_ under the MIT licence (\u00a2 Edinburgh Genome Foundry), everyone is welcome to contribute !\n\nBioprinter was written at the Edinburgh Genome Foundry by Zulko_ after an original idea and Matlab code by Mike Shen (`Mike's project on Github <https://github.com/mshen5/BioPointillism>`_).\n\nInstallation\n--------------\n\n\nIf you have PIP installed: ::\n\n    (sudo) pip install ez_setup bioprinter\n\nOr unzip the source code in a directory and type in a terminal: ::\n\n    sudo python setup.py install\n\n\nUsage\n--------\n\nIn the same folder as your code, place an image. It can have any resolution, but keep in mind that the width/height ratio of the plate it is printed on is 1.5. Make sure that a specific color is used to mark the un-pigmented background of the image, here we use blue:\n\n.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/dolly.jpeg\n    :align: center\n\nThen write the following code in ``dolly.py``:\n\n.. code:: python\n\n    from bioprinter import bioprint\n\n    bioprint(\n        image_filename=\"../docs/_static/images/dolly.jpeg\",\n        output_filename=\"dolly.csv\",\n        bg_color=[0, 0, 255], # blue background represents empty wells\n        pigments_wells={\"A1\": [0, 0, 0],  # black yeast in source well A1\n                        \"A2\": [250, 120, 10],  # orange yeast in well A2\n                        \"A3\": [255, 255, 255]},  # white yeast in well A3\n        quantified_image_filename=\"dolly_preview.jpeg\"\n    )\n\nExecute in a terminal with ``python dolly.py``. This will produce a ``dolly.csv`` file as well as a preview image of the final printing (so that you can check if the image looks good at this low resolution).\n\nPrepare a source plate with the right pigmented yeasts in wells A1, A2, A3, use an agar plate as the destination plate, and feed ``dolly.csv`` to the `Labcyte Echo <http://www.labcyte.com/products/liquidhandling/echo-555-liquid-handler>`_. Once the printing is finished, incubate 2 days at 30C (it would be one day at 37C for bacteria). Enjoy the result !\n\n\n.. _here: http://edinburgh-genome-foundry.github.io/bioprinter/\n.. _Zulko: https://github.com/Zulko/\n.. _Github: https://github.com/Edinburgh-Genome-Foundry/bioprinter\n",
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