Skip to main content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.


The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Low-Cost, High-Throughput, Automated Counting of Bacterial Colonies



Matthew L. Clarke, Robert L. Burton, A. N. Hill, Maritoni A. Litorja, Moon H. Nahm, Jeeseong Hwang


Research involving bacterial pathogens often requires enumeration of bacteria colonies. Here we present a low-cost, high-throughput colony counting system consisting of colony counting software and a consumer-grade digital camera or document scanner. We demonstrate that this software, called NICE (NIST s Integrated Colony Enumerator), can count bacterial colonies as part of a high-throughput multiplexed opsonophagocytic killing assay (MOPA), which is used to characterize pneumococcal vaccine efficacy. The results obtained with NICE correlate well with the results obtained from manual counting, with a mean difference of less than 3%. NICE is also rapid; it can count colonies from multiple reaction wells within minutes and export the results to a spreadsheet for data processing. As this program is freely available from NIST, NICE should be helpful in bacteria colony enumeration required in many microbiological studies, and in standardizing colony counting methods.
Cytometry Part A


bacteria, colony counting, imaging, MOPA, pneumoniae, software, vaccine
Created January 5, 2010, Updated January 27, 2020