Manually Select Area for Leaf Area Calculation

imagej

#1

Hey there,

I have been using ImageJ with a macro plug-in to calculate leaf area for a variety of species. This has proven mostly effective, however, some scans have proven more difficult than others. That is, some scans are more difficult to black out than others (while processing the scans using macro plug-in). I’ve tried adjusting the threshold, however this isn’t producing the desired output. I’m hoping someone can provide a protocol or step-by-step instructions to manually calculate leaf area of these difficult scans.

Thanks for any and all help.

Best,
Katie


Calculate Leaf Area in ImageJ
#2

Hi !
What seems to be the main problem? And we could really use a PNG or Tif sample image if possible. JPEG is no good for analyzing, but if that’s all you have send it then. Please

Bob


#3

Hi Bob,

This is an example of what I have. I hope this helps!

Thank you,
Katie


#4

Excellent! Just invert from the Edit menu, mean while I’ll see if some other procedure is better. Will get back with you soon.
Bob


#5

Hello again Katie,
Is this good enough?
Bob


#6

Hi Bob,

It’s certainly improved. The end goal is to insure the “stems” are included in the leaf area calculation. In the image you provided, some portions of the stems are blacked out. Do you think it is a possible to calculate the leaf area with those parts of the stem included?

I have several similar scans with this lighter stem color. Again, any and all help is greatly appreciated! Thank you.

Cheers,
Katie


#7

Hi Katie,
First I inverted the image with Edit > invert, Then used the “Wand” tool set at 20 and hit the background, Edit > clear all , then refined the left over lighter areas with the wand tool again, and finally I inverted back to normal and threshold the image to suit. This should work with your images. If not let me know and I will give it another go.

Bob


#8

Hi Bob,

Excellent - this is hugely helpful. Thanks for the pro tips!

Katie


#9

Just for the record:

This thread continues here
https://forum.image.sc/t/calculate-leaf-area-in-imagej/20776?u=herbie

Herbie