Annotated dataset for deep-learning-based bacterial colony detection

Quantifying bacteria per unit mass or volume is a common task in various fields of microbiology (e.g., infectiology and food hygiene). Most bacteria can be grown on culture media. The unicellular bacteria reproduce by dividing into two cells, which increases the number of bacteria in the population. Methodologically, this can be followed by culture procedures, which mostly involve determining the number of bacterial colonies on the solid culture media that are visible to the naked eye. However, it is a time-consuming and laborious professional activity. Addressing the automation of colony counting by convolutional neural networks in our work, we have cultured 24 bacteria species of veterinary importance with different concentrations on solid media. A total of 56,865 colonies were annotated manually by bounding boxes on the 369 digital images of bacterial cultures. The published dataset will help developments that use artificial intelligence to automate the counting of bacterial colonies.