bioprinter 0.1.5

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Bioprinter (webpage here) is a Python package for producing 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).

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

These 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).

Bioprinter is released on Github under the MIT licence (Copyright 2015 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 (project on Github).

Installation

If you have PIP installed:

pip install ez_setup bioprinter

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

python setup.py install

Usage

The image file to be printed can have any resolution, but note that the width/height ratio of the plate the image is printed on is 1.5. Ensure that a specific color is used to mark the un-pigmented background of the image, here we use blue:

Run the following code in Python or save in dolly.py:

from bioprinter import bioprint

bioprint(
    image_filename="/path/to/image/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"
)

The saved script can be executed 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 Acoustic Liquid Handler (tested with Labcyte Echo 555 Series). Once the printing is finished, incubate 2 days at 30C (it would be one day at 37C for bacteria). Enjoy the result!