Software for counting colonies?

huberman at huberman at
Tue Dec 3 18:21:14 EST 1996

In article <57tocc$itc at>, karthi at wrote:

> Hi everyone,
> We are doing some genetics experiments that requirs counting colonies on 100s 
> of plates each time. We have the facility for capturing images of these
> and storing them digitally. I am wondering if there are any software 
> commercial/ shareware/ freeware that will count the colonies from these 
> images? 
> Any pointers will be greatly appreciated
> Thanx very much
> Karthi. R
> ---------------------------------------------------------------------------
> Karthikeyan Ramachandran Ph.D
> Research Fellow, Rm. No. SA136
> School of Biological and Chemical Sciences
> Faculty of Science and Technology               Phone (Off) (052) 271 406
> Deakin University                       Phone (Res) (052) 419 806
> Geelong, Victoria                       Fax (052) 272 022
> Australia 3217                          e-mail karthi at
> Home page                     

Dear Rathi,

   If you have a Macintosh, there are two routes. First, the free one. NIH
Image is a good image analysis program available for free from the
following FTP site: At the same
site are one or two "macros" for the program that permit counting objects,
even colonies.

   In my own work, I have obtained better results with a "macro" that I
wrote myself for the excellent image analysis program, IPLab Spectrum.
This program is available from:

Signal Analytics Corporation
440 Maple Avenue East, Suite 201
Vienna, VA  22180

   If you have this program, my macro can help you out. Just send me an
e-mail message (huberman at, and I'll send it to you.

   Note: neither my macro nor the NIH Image macros are good at counting
crowded colonies. In both cases, the majority of colonies on the plate
must be single--they must not touch each other.

   I hope this information helps you.

Sincerely yours,
Joel Huberman

More information about the Yeast mailing list