Using level of red pixels in photo to measure growth

Using level of red pixels in photo to measure growth

Hi. I have taken several images showing growth of microscopic red algae on shell substrata over time, and want to investigate if the level of red pixels in the photos can be used as a measurement for growth. Therefor the red-pixels in the area where the algae is growing is the area of interest to me, and I would like to find the number fo red pixels in this area (picture 1), but at the same time being able to compare it with the level of red pixels in other pictures of the same shell (E.g. Picture 2,), to detect growth over time.

However i’m new to ImageJ/Fiji and would be grateful for some suggestions on how this program could be helpful.

I have already tried looking at the “color histogram” in the different photos (both using the original photo, using ROI covering the area of interest, and splitting the photo (Split channel) into red, green and blue pixels), but i’m not able to detect a change in red pixels based on this data.

They way i understand it I may have to furter prosess the photos to detect a change in level of red pixels. My question is then: How can i do this in a good way? Some of the challenges I would have to account for is the flash and shadow part of the photo (the area of both flash and shadow is changing some between the different photos).

The pictures is taken using the same distance and light conditions, but as you can see there is some some minor adjustments.

As stated pervious, I’m new to imageJ and might need a step by step explanation.

Picture 1 (low growth of alga)
10.30_1.3|375x500

Picture 2 (“high” growth of alga)
11.16_1.3 !

What do you mean by levels of red pixels?
One way would be to use the color threshold to quantify the area.
colorThres

Image > Adjust > Color Threshold…
But I would be careful!
One thing is the variability of the imaging condition. That would influence the color too. Thus a color reference in the image or really stable conditions would be good.
The other thing that I could imagine is that the color actually changes as a function of the growth… that is something I would at least look out for.

Alternatively you could segment using a grey scale image to get an area measurement.