CellProfiler and ImageJ

[WoodlandBrew]

What are people using these days to automate yeast cell counts? I'm collecting several hundred images for an experiment that I am running and am looking record viability, cell size, and hopeful be able to identify abnormally shaped cells. I've been doing it manually, which isn't too bad, but am looking for something that will remove some of the subjectivity of a cell count, and maybe even speed the process. With ImageJ I think I could set up a macro to extract the data I want. Is CellProfiler any better?

 

[supermutantbrewmaster]

Hey Matt. There are some sperm cell counting apps used with ImageJ for research in fish sperm viability. I'm pretty sure the app is called CASA.

 

[WoodlandBrew]

Thanks Jake! I'll check that out.

 

[WoodlandBrew]

Well, I got automated cell counts working pretty well with ImageJ. Here are the details including macros:
http://www.woodlandbrew.com/2015/02/automated-cell-counting-of-yeast-using.html

 

[biertourist]

This is really great; I've been waiting to see scripts and an easy-to-implement solution made available for the HomeBrew community for quite sometime.

Glad to see you've been working on it.

-I actually repurposed a trial copy of an off-the-shelf star counter for taking images from home telescopes and tweaked some of the settings to get it to instead count yeast cells but it had a lot of false positives and I really couldn't be bothered to make it work any more accurately.

The professionals use ImageJ when they're not using insanely expensive commercial solutions so I always hoped someone would dumb it down enough for even me to use.


Adam

 

[WoodlandBrew]

Thanks! I hope it works for you, but I suspect it may take some tweaking. I'd be very interested to hear how it works for you.