Analyzing RGB color along freehand line

Sample image


Background

Hi! I’m trying to analyze color changes in these worms throughout an experiment.

Analysis goals

I want to be able to get the RGB values across a single worm, selected via a freehand line. The images I have are of multiple worms per image and are also on a somewhat heterogenous background (a petri dish with shadows and other color differences across it, as you can hopefully see in the images) and so far I’ve only been able to get data for the entire image or a square ROI (which won’t work due to the background and some of the worms are very close to each other). I’ve been able to analyze this for gray intensity across the line I’ve drawn (see image above), but I would like similar values for RGB or calculate the histogram of RGB values only across the freehand line I’ve drawn. I’ve been able to export data on the histogram of RGB values but only for the full image.

Challenges

Things I’ve tried: I’ve downloaded and installed the RGB Measure (RGB Measure) and Color Histogram (Color Histogram) plugins, but I’m not sure how to use these to analyze only the pixels across the line I’ve drawn. I can get RGB histogram values across the whole image. I can also get gray values across the line (see larger image with whole petri dish - plot to the right of dish) by selecting Analyze > Plot profiles, but I want similar data for RGB values or histogram values for RGB. Ideally, I’d get RGB values across the distance of the line (like those gray values) but that’s not 100% necessary - I can make do with a histogram of the RGB values across the line.

“This Plugin draw the Red, Green and Blue profile plot of an RGB image on the same Plot, for each type of line selection. This profile is refreshed when a new selection is made. Large parts of this code were taken from plugins by Wayne Rasband.”

2 Likes

@gabriel Yes this looks like exactly what I want! Thank you so much! I’m able to make a plot of the RGB values across distance, which is great, but how do I export the data? I can’t find any help documents online.