I was not having issues until this week, in which leaves reached the pot edge, and tools as Make Binary or Threshold take leaf and pot as a unit, despite the color of these are pretty different...
Dear David,
To solve this problem we measured the total rosette area and at the final timing point we scanned each leaves and measure the individual surface with image J.
You can try to change the color mode in Threshold from HSB to RGB and/or change more than one parameters (H and S or R and G) together. Also, each parameter has 2 sliders each side, so use them together to narrow down say only green color and excluding both red and blue in H. If the colors of the pot and the leaf really are different I think it is possible to separate them.
Hey. These are the pictures of normal and edited image. I have been trying all threshold parameters and did not work it. Green leaves merge with white pots :(
Use this setting:
Hue: 42 - 80
Saturation: 50 - 255
Brightness: 100 - 255
It's not perfect, but acceptable
There is a program called Leaf-GP made for Arabidopsis
https://www.biorxiv.org/content/10.1101/180083v1.full.pdf
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