bioprinter 0.1.0

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Bioprinter (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.

Here are two examples of bio-art:

Dolly drawn with baker yeast (white), violacein-producing yeast (black), and carotene-producing yeast (orange)

England flag drawn with 3 different strains of the bacterium E. coli.

Bioprinter is released on Github under the MIT licence (¢ Edinburgh Genome Foundry), everyone is welcome to contribute !

Bioprinter was written at the Edinburgh Genome Foundry by Zulko after an original idea and Matlab code by Mike Shen (Mike’s project on Github).

Installation

If you have PIP installed:

(sudo) pip install ez_setup bioprinter

Or unzip the source code in a directory and type in a terminal:

sudo python setup.py install

Usage

In 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:

Then write the following code in dolly.py:

from bioprinter import bioprint

bioprint(
    image_filename="../docs/_static/images/dolly.jpeg",
    output_filename="dolly.csv",
    bg_color=[0, 0, 255], # blue background represents empty wells
    pigments_wells={"A1": [0, 0, 0],  # black yeast in source well A1
                    "A2": [250, 120, 10],  # orange yeast in well A2
                    "A3": [255, 255, 255]},  # white yeast in well A3
    quantified_image_filename="dolly_preview.jpeg"
)

Execute 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).

Prepare 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. Once the printing is finished, incubate 2 days at 30C (it would be one day at 37C for bacteria). Enjoy the result !