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bioprinter

🖨️ Print pictures with living micro-organisms!

https://github.com/edinburgh-genome-foundry/bioprinter

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
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    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.5%) to scientific vocabulary

Keywords

art biology design
Last synced: 6 months ago · JSON representation

Repository

🖨️ Print pictures with living micro-organisms!

Basic Info
Statistics
  • Stars: 14
  • Watchers: 3
  • Forks: 4
  • Open Issues: 1
  • Releases: 4
Topics
art biology design
Created almost 10 years ago · Last pushed 11 months ago
Metadata Files
Readme

README.rst 

.. raw:: html

    

    Bioprinter logo
    


    



.. image:: https://github.com/Edinburgh-Genome-Foundry/bioprinter/actions/workflows/build.yml/badge.svg
    :target: https://github.com/Edinburgh-Genome-Foundry/bioprinter/actions/workflows/build.yml
    :alt: GitHub CI build status

.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/bioprinter/badge.svg?branch=master
   :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/bioprinter?branch=master


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:

.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_dolly.jpeg
    :align: center

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


.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_england.jpeg
    :align: center

    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 license (Copyright 2015 Edinburgh Genome Foundry, University of Edinburgh), 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
------------

Install with PIP: ::

    pip install bioprinter


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:

.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/dolly.jpeg
    :align: center

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

.. code:: python

    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!


.. _here: http://edinburgh-genome-foundry.github.io/bioprinter/
.. _Zulko: https://github.com/Zulko/
.. _Github: https://github.com/Edinburgh-Genome-Foundry/bioprinter

Owner

  • Name: Edinburgh Genome Foundry
  • Login: Edinburgh-Genome-Foundry
  • Kind: organization
  • Email: egf-software@ed.ac.uk
  • Location: Edinburgh, UK

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 40
  • Total Committers: 5
  • Avg Commits per committer: 8.0
  • Development Distribution Score (DDS): 0.525
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Zulko v****r@g****m 19
Peter Vegh p****h@p****k 10
Valentin Zulkower v****r@g****m 9
Zulko v****r@g****l 1
Zulko Z****o 1
Committer Domains (Top 20 + Academic)
posteo.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 3
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 2.67
  • Average comments per pull request: 1.67
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ecederstrand (2)
  • dylanasimov (1)
Pull Request Authors
  • Zulko (1)
  • ecederstrand (1)
  • veghp (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 52 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
pypi.org: bioprinter

Print pictures with living micro-organisms!

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 52 Last month
Rankings
Dependent packages count: 7.3%
Forks count: 15.4%
Stargazers count: 16.1%
Average: 31.2%
Downloads: 48.8%
Dependent repos count: 68.5%
Maintainers (1)
EdinburghGenomeFoundry
Last synced: 6 months ago

Dependencies

.github/workflows/build.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • coverallsapp/github-action v2 composite
.github/workflows/document.yml actions
  • sphinx-notes/pages v3 composite
.github/workflows/publish.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pypa/gh-action-pypi-publish release/v1 composite
docs/requirements.txt pypi
  • sphinx_rtd_theme *
pyproject.toml pypi
  • Pillow *
  • numpy *