AssiST: convolutional neural network for analysis of antibiotic susceptibility testing.

Summary: Antibiotic susceptibility testing (AST) is routinely used to evaluate microbial responses to antimicrobials. We present AssiST, a convolutional neural network (CNN) pipeline that classifies microbial growth in scanned 96-well broth microdilution plates to infer drug susceptibility at scale. AssiST accommodates diverse growth morphologies and supports a user-configurable mapping from phenotype to susceptibility calls, enabling flexible use across microorganism species, media types, and drugs. AssiST allows labs to convert flatbed-scanner images into reproducible drug sensitivity readouts with a standard personal computer. Availability and implementation: AssiST is distributed as a MATLAB library and is freely available for non-commercial use. Code, documentation, and training/inference instructions are available at https://github.com/Mitchell-SysBio/AssiST/. We also provide pre-trained models and a library of sample images. The software accepts image files from standard flatbed scanners. We commit to maintaining the repository for at least 2 years post-publication.