A Convenient Way of Counting CFU (to be continued)


Today, I am going to talk about a convenient way of counting CFU. In microbiology, a colony-forming unit (CFU) is a unit used to estimate the number of viable bacteria or fungal cells in a sample. We are, recently, testing the bactericidal properties of the photosensitizer that we have synthesized. Hence, we spent lots of time to count the CFU with marking pen and Lab Hand Tally Counter like this (it seems kind of cute, emmmm).

Lab Hand Tally Counter

So, I was wondered if there is a more feasible way to do this job efficiently. Then I googled an open-source software named ImageJ which can do that work automatically. There, nevertheless, are inevitably problems with the accuracy of the results by using a software to count it. I'll talk about that later. Now, let's learn how does it work first.

Application Method


Above of all, we need to take a photograph of Petri dishes that we've already inoculated with bacteria (like below).

Software Installation

We can get ImageJ on its official website or GitHub. After decompressing, we can open the software directly.

After that, you will get a dashboard like below.

Processing Photos

Open your photo by "File → Open".

Select the second tool - "oval" - to select the area where the bacteria are.

Then, click "Edit" → "Clear Outside" to clear excess areas.

For separating the colonies from the background more clearly, we use "Image" → "Adjust" → "Brightness/Contrast..." to change them.

We adjust these four property (the main adjustments are the above two, from my experience) to make it become black and white.

When you think it is appropriate, click "Set" and "OK". Then we use the "Threshold" to binarize the color of this photo, which you can find it in the "Image" → "Adjust" → "Threshold".



Author: Xuan
Copyright: CC BY-NC-SA 4.0
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