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NIST's Integrated Colony Enumerator (NICE)


Enumeration of bacterial colonies on an agar plate is simple in concept, but automated colony counting is difficult due to variations in colony color, size, shape, contrast, and density, as well as colony overlap. Furthermore, in applications where high throughput is essential, it is critical to employ a fast and user-friendly automated technique that does not compromise counting accuracy. We have developed a colony counting program, NIST’s Integrated Colony Enumerator (NICE), designed to count dark colonies from multiple regions of interests on an agar plate. Images can be cost effectively acquired by a digital camera or a desktop scanner and imported into NICE. Multiplexed, high throughput standardized assay formats such as the multiplexed opsonophagocytic killing (MOPA4) assay can be readily counted by NICE.

There are two software files required to run NICE. There is also one supplementary file and documentation. Descriptions of these files are available below, and the files can be downloaded from the following ftp site, click here to download.

MCRInstaller.exe - Installs the MATLAB complier engine, version 7.9. The complier is available for free.

NICE_xxx.exe - Launches NICE. - NICE source files written in MATLAB (.m and .fig files). - Demonstration images.

NIST manual.pdf - Documentation for the software.

To be notified of updates to NICE, please send your name and organization in an email to

Sample Screenshots:


 NICE sample window

The main window of NICE is shown with a counted 24-spot plate. The blue numbers are the number of colonies counted within the regions of interest (blue boxes). The histogram near the bottom displays the image properties within the analysis area (pink box).


Version: 1.2

Last Updated: August 11, 2010

Type of software: Complied MATLAB executable


Matthew Clarke

Jeeseong Hwang


32-bit Windows

Licensing info:

NIST’s Integrated Colony Enumerator (NICE) software was developed at the National Institute of Standards and Technology by employees of the Federal Government in the course of their official duties. Pursuant to Title 17 Section 105 of the United States Code this software is not subject to copyright protection and is in the public domain. Support for this project was provided in part by PATH. The views expressed by the developers of the software do not necessarily reflect the views of PATH. NICE is an experimental system. Neither NIST nor PATH assumes any responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. We would appreciate acknowledgment if the software is used. This software can be redistributed and/or modified freely provided that any derivative works bear some notice that they are derived from it, and any modified versions bear some notice that they have been modified.


Quantum Electronics and Photonics Division
Robert Hickernell, Chief

Molecular and Biomolecular Project
Kimberly Briggman, Leader

NIST's Integrated colony enumerator (NICE):
Jeeseong Hwang
303-497-6588 Telephone

General Information:
325 Broadway MS815.01
Boulder, CO 80305
303-497-7287 Telephone