Cell counting program needed

Question

[simon.polak]

Hello there,

I sometimes perform this single cell assay where I take pictures of a micro-array with yeast cells and I need to count the cells. It's a hell of a lot of work, so I could use a computer program to do it for me. I know that cell-counting programs already exist, but none I found so far seems to meet my criteria. They are as follows:

• Only the dead cells, which can be identified as they are marked with a fluorescent agent and glow, should be counted. In other words, only the cells that light up with a certain intensity should be counted (living cells might light up a tiny bit too).

• The micro-array is covered with wells and only the dead cells -inside- those wells should be counted. The edges of the wells tend to light up, so the program should be able to distinguish the wells from the dead cells. Also, the wells are all regularly interspaced, as if located on the vertices of a grid.

• Some debris particles might light up too and should not be counted.

Can anyone recommend me a program that could do this counting for me? Or can you tell me how to contact someone who could design this for me? If this helps, I work in Belgium.

Answer 1

[Carambakaracho]

Hi simon,

my image analysis skills are a bit rusty, but maybe ImageJ can help you when you combine a

• Background substraction (scroll down a bit to the section) to remove the uneven background
• Top-hat transform to separate wells from cells
• use one ofthe cell count techniques described here: https://www.unige.ch/medecine/bioimaging/files/3714/1208/5964/CellCounting.pdf

[simon.polak]

Thanks for this. That background substraction seems useful since the 'masking unwanted regions' allows me to exclude everything from the counting except for a selected region of my choice. But I can't seem to manage to select multiple regions outside which I don't want to count, instead of only one. Any ideas?