Yeast cell counting in a droplet

Hello all! I would like to know, how can I calculate number of yeast cells in a droplet over time. Any help would be greatly appreciated as I am new to this S/W

Hi @Piyush_Katakwar

Welcome to the Forum! In order to better help you… it would be great if you could share some raw image files with us - that is the best way to get help. So post an example image here and just detail exactly what you want to measure.

eta :slight_smile:

Hey @etadobson
Thanks for the quick response. I have attached an image with a trapped droplet. I want to calculate no. of yeast cells in this image. Then I would like to have a model which can calculate these cells for different images in a image sequence.


I’ll start with saying that jpeg is really not the best file format for saving your data. There are many reasons - you can read more here. In the future - just be sure to save your images as TIFFs… that is the best practice for quantification analyses.

Follow this Segmentation link… Read up on Analyze Particles, Set Measurements, ROI Manager … and you’ll be ready to start segmenting your yeast cells. You might also have some luck with Color Threshold.

Another great segmenting tool is the Trainable Weka Segmenation (TWS) Plugin. Read up on it here. That might be a good option for you to segment your yeast cells… then apply that same classifier on multiple images.

In any case - be sure to document the exact steps you do - for yourself in the future and sharing with others… To help with this - you can start looking into macros to script your workflow. This workshop on scripting in imagej might also be of use. Then you can apply your analysis workflow to multiple images too!!

Hope this helps with getting you started. And post more questions if and when you need.