How to Count Colonies on Agar Plates: A Complete Guide

Get access For Free to our comprehensive How to Count Colonies on Agar Plates PDF Guide (19 pages) put together by our specialists, Dr. Katja Schulze, who specialized in bioinformatics and image recognition of microscopic images, and Dr. Ulrich M. Tillich, who specialized in laboratory automation!

Counting colonies on an agar plate is a crucial task in laboratory work, especially in microbiology. It is also a sensitive, time-consuming, and error-prone process that can always benefit from improvement.

It is generally accepted that, to obtain a statistically reliable estimate of the quantity of bacteria in your sample you should select for counting the plates that contain between 30 and 300 colonies.

This leaves you with a significant quantity of colonies to count, which is made even more difficult by the fact that the way the colonies will end up looking after the incubation period can vary greatly in:
– shape (they can be circular, irregular, filamentous, or even rhizoid);
– color (ranging from translucent or white to pigmented shades like yellow, pink, red, or even metallic tones);
– size;
– texture and elevation (smooth, rough or wrinkled in texture and raised, flat or convex in elevation);
– transparency (some might me translucent, while others are opaque);
– and in the type of margin they have (entire, undulate, lobate, or filamentous).

Now, the general recommendation for counting colonies on agar plates is to start counting from the outer perimeter of the plate, moving toward the center to ensure you don’t miss any colonies. However, there are a few more specific methods and steps you can follow to make this process easier and more accurate.

And, in this guide on how to count colonies on agar plates, we’re diving into them:


  • Optimizing the light source
  • Marking counted colonies correctly
  • Tips on avoiding over-counting


  • The Quadrant Method
  • The Zigzag Method
  • The Grid Method
  • The Spiral Plate Method

This detailed guide contains recommendations you can implement immediately to make your life easier and return more accurate counts. It will help you whether you’ve been counting colonies for a while and you just want to improve your method, you’re just starting to do colony counts now or you’re training someone else to do it.

If you have any additional questions whatsoever or you’re interested in significantly speeding up lab work by using our Automated Colony Counter, do not hesitate to send us an email at [email protected] and we’ll be happy to assist you!

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