aigarmic 1.0.0

Machine-learning assisted agar dilution MIC

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 ([e-mail]).

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://10.17638/datacat.liverpool.ac.uk/2631.

License

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