Assessing Foundation Models for Mold Colony Detection with Limited Training Data

The process of quantifying mold colonies on Petri dish samples is of critical importance for the assessment of indoor air quality, as high colony counts can indicate potential health risks and deficiencies in ventilation systems. Conventionally the automation of such a labor-intensive process, as well as other tasks in microbiology, relies on the manual annotation of large datasets and the subsequent extensive training of models like YoloV9. To demonstrate that exhaustive annotation is not a prerequisite anymore when tackling a new vision task, we compile a representative dataset of 5000 Petri dish images annotated with bounding boxes, simulating both a traditional data collection approach as well as few-shot and low-shot scenarios with well curated subsets with instance level masks. We benchmark three vision foundation models against traditional baselines on task specific metrics, reflecting realistic real-world requirements. Notably, MaskDINO attains near-parity with an extensively trained YoloV9 model while finetuned only on 150 images, retaining competitive performance with as few as 25 images, still being reliable on $\approx$ 70% of the samples. Our results show that data-efficient foundation models can match traditional approaches with only a fraction of the required data, enabling earlier development and faster iterative improvement of automated microbiological systems with a superior upper-bound performance than traditional models would achieve.