AIgarMIC

Introduction

AIgarMIC is a Python package and collection of commandline scripts designed to facilitate the automation of agar dilution minimum inhibitory concentration image interpretation.

AIgarMIC has the following features:

• Automated image processing of agar dilution plates in the following format (note the use of an anchoring black grid to delineate colonies):

• Flexible MIC calculation algorithm with ability to disregard inhibited growth
• Quality assurance metrics to ensure MIC predictions
• Pre-trained models and example datasets
• Scripts to support custom model training

Documentation

The full documentation for AIgarMIC can be found at:

https://aigarmic.readthedocs.io/en/latest/

Installation

To install AIgarMIC, follow the instructions below:

https://aigarmic.readthedocs.io/en/latest/installation.html

Usage

To use AIgarMIC, follow one of the typical workflows described below:

https://aigarmic.readthedocs.io/en/latest/introduction.html#typical-workflows

Author information

The lead developer of AIgarMIC is Alessandro Gerada (https://github.com/agerada/ and https://agerada.github.io/), University of Liverpool, UK (alessandro.gerada@liverpool.ac.uk).

Cite

If you are using AIgarMIC in your research project, please cite:

@article{geradaAIgarMICPythonPackage2024,
  title = {{{AIgarMIC}}: A {{Python}} Package for Automated Interpretationof Agar Dilution Minimum Inhibitory Concentration Assays},
  shorttitle = {{{AIgarMIC}}},
  author = {Gerada, Alessandro and Harper, Nicholas and Howard, Alex and Hope, William},
  year = {2024},
  month = sep,
  journal = {Journal of Open Source Software},
  volume = {9},
  number = {101},
  pages = {6826},
  issn = {2475-9066},
  doi = {10.21105/joss.06826},
  urldate = {2024-10-07},
  copyright = {http://creativecommons.org/licenses/by/4.0/},
  file = {/Users/agerada/Library/Mobile Documents/com~apple~CloudDocs/Zotero/Journal Article/Gerada et al_2024_AIgarMIC.pdf}
}

To cite the validation data and developmental approach described in the AIgarMIC validation manuscript, please cite:

@article{geradaDeterminationMinimumInhibitory2024,
  title = {Determination of Minimum Inhibitory Concentrations Using Machine-Learning-Assisted Agar Dilution},
  author = {Gerada, Alessandro and Harper, Nicholas and Howard, Alex and Reza, Nada and Hope, William},
  editor = {Shier, Kileen L.},
  date = {2024-03-22},
  journaltitle = {Microbiology Spectrum},
  shortjournal = {Microbiol Spectr},
  pages = {e04209-23},
  issn = {2165-0497},
  doi = {10.1128/spectrum.04209-23},
  url = {https://journals.asm.org/doi/10.1128/spectrum.04209-23},
  urldate = {2024-04-02},
  langid = {english}
}

External links

The manuscript describing the validation of AIgarMIC can be found at: https://doi.org/10.1128/spectrum.04209-23. Optional asset data is available at: https://doi.org/10.17638/datacat.liverpool.ac.uk%2F2631.

Contributing

We welcome contributions to AIgarMIC. Please follow our contributing guidelines.

License

AIgarMIC is provided under the GNU General Public License v3.0. For more information, see the LICENSE file.