SA measurements with threshholding help


Hi all,

Very new to this, I’m trying to measure the surface area of some small aquatic ferns (Azolla) with ImageJ but having issues. Using 'Adjust > ‘Color threshhold’ (after setting scale and cropping) I can highlight roughly 90-95% of the area i want simply sliding only the saturation bar (and i can get similar results with brightness only), but I have 2 issues: a) the darker growing tips don’t get included (which i want) while the roots below do get included (which i don’t want). See pic below for reference (different image to top one, i know).

I have multiple images so obviously trying to keep it as simple as possible.

Unfortunately the Hue bar doesn’t work especially well for me. Probably due to poor photography setup, most of the pixels representing the Azolla are up around the yellow-orange spectrum, not green as i’d hoped. The blue-green pixels in the picture below represent the background,
Also the dark growing tips complicate it again.

As mentioned i’m very new to this so if there’s any functions within ImageJ/Fiji or tips you can offer that would help to get more accurate measures i’d really appreciate the help :slight_smile:


I would use a scanner for the measurements (where you also get the dpi settings in most scanner images) as I did in the past with roots. Your plants a very small and suitable for a scanner setup.

Another problem with this pictures are that they have (if you can’t repeat the scanning/digitalization) a perspective distortion introduced by the wrong camera angle. To measure the correct area they have to be rectlinear.

It depends how exact you want to have your measurements (it might be that you can statistically calculate the measurements error).

So I would correct the perspective distortion, too. Probably for every image.

To segment the images you could also try the quite popular segmentation plugin: