I'm trying to measure the average raft culture thickness from my 3D-organotypic cultures using ImageJ but haven't been very successful. Can anyone suggest a tool or method for this? I've uploaded one of my images as an example. Images were taken using Zeiss slide scanner.
Thank You
What exactly are you trying to achieve in ImageJ and what is the problem you are having? Do you have a calibration slide to get the length unit (e.g. micron) to pixel conversion?
I'm assuming you want to measure the width of that stained cell layer. It's not uniform, so are you looking for an average?
Once you have the calibration information you can manually make measurements using the line tool and the Measure options under the Analyze menu.
To get more of an average quicker, you could threshold the image and obtain the area of the stained layer, then divide by the length--either use the Feret diameter, measure manually or use skeleton analysis. Area/length will give you avg. width or in this case thickness.
Thank you Peter, I wanted to do exactly what you described. I'll try what you've suggested.
Good luck. If you still have problems, post and I can walk you more step-by-step.
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