Machine learning for enumeration of cell colony forming units

• Published in: Visual computing for industry, biomedicine and art Vol. 5; no. 1; pp. 26 - 8
• Main Author: Zhang, Louis
• Format: Journal Article
• Language: English
• Published: Singapore Springer Nature Singapore 05.11.2022; Springer Nature B.V; SpringerOpen
• Subjects: AI-based Image Analysis; Algorithms; Automation; Blue/white screen; CAE) and Design; Colonies; Colony count; Colony forming unit; Computer Graphics; Computer Imaging; Computer Science; Computer-Aided Engineering (CAD; Digital imaging; Enumeration; Genes; Genomics; Image analysis; Image Processing and Computer Vision; Image segmentation; Machine learning; Media Design; Mutagenesis; Mutation; Original; Original Article; Pattern Recognition and Graphics; Proteins; Software; Unsupervised learning; Vision; Watersheds; Colony forming unit; Image analysis; Enumeration; Colony count; Blue/white screen
• ISSN: 2524-4442; 2096-496X; 2524-4442
• DOI: 10.1186/s42492-022-00122-3

As one of the most widely used assays in biological research, an enumeration of the bacterial cell colonies is an important but time-consuming and labor-intensive process. To speed up the colony counting, a machine learning method is presented for counting the colony forming units (CFUs), which is referred to as CFUCounter. This cell-counting program processes digital images and segments bacterial colonies. The algorithm combines unsupervised machine learning, iterative adaptive thresholding, and local-minima-based watershed segmentation to enable an accurate and robust cell counting. Compared to a manual counting method, CFUCounter supports color-based CFU classification, allows plates containing heterologous colonies to be counted individually, and demonstrates overall performance (slope 0.996, SD 0.013, 95%CI: 0.97–1.02, p value < 1e-11, r = 0.999) indistinguishable from the gold standard of point-and-click counting. This CFUCounter application is open-source and easy to use as a unique addition to the arsenal of colony-counting tools.