Database of Petri plates with e.coli,p.aeruginosa and s.aureus cataloged in this way: attributing number, bacterial species and total manual count to each image, e.g., CEMTimages_0278_EC_C76, where 0278, EC and C76 meaning the image number, bacterial species and total count, respectively. The built dataset consisted of about 1150 labeled images with approximately the same number of images for each bacterial species to attain a balanced database. More info check: https://doi.org/10.3390/bioengineering9070271