Calculating Leaf Area as a whole

I am new to Image J but am in need of Leaf area analysis from a photo attached below. I am having a difficult time separating the leaf material from the medium. Any thoughts on how to do this? DSC00497

Good day,
@RollTigs

You can take a look at this old tread


Regards

Dear RollTigs,
Did you try the weka trainable method
Trainable_Weka_Segmentation

Citation
The Trainable Weka Segmentation is a Fiji plugin that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations. Weka (Waikato Environment for Knowledge Analysis) can itself be called from the plugin. It contains a collection of visualization tools and algorithms for data analysis and predictive modeling, together with graphical user interfaces for easy access to this functionality. As described on their wikipedia site, the advantages of Weka include

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Hi
@RollTigs

Weka does better than below!! :shushing_face:

macro " Leaf Area"
{
requires("1.52u");
setBackgroundColor(0, 0, 0);
setOption("BlackBackground", true);
time0=getTime();
img=getImageID();
// Start batch mode
setBatchMode(true);
selectImage(img);
run("Duplicate...", "title=1");
close("\\Others");
run("Duplicate...", "title=2");
run("Lab Stack");
wait(1000);
run("Stack to Images");
selectWindow("a*");
setAutoThreshold("Default");
//run("Threshold...");
run("Duplicate...", "title=mask ");
run("Convert to Mask");
run("Set Measurements...", "area add redirect=None decimal=2");
run("Analyze Particles...", "size=100-Infinity display exclude add");
run("Create Selection");
selectImage("1");
run("Restore Selection");
run("Clear", "slice");
setBatchMode(false);
// End of batch mode
run("Select None");
time1=getTime();
// Length of the proceedings

length=(time1-time0)/1000;
print("length=",length+"secondes");
exit();
}

Greetings

Alex.h,
I am not familiar with Weka, but what you showed on the image is something that looks like would be useful in calculating the leaf area. If there are nay other tips you may have to getting to the point you have gotten to in the image above, it would be helpful as I have many images I need to have formatted like this to analyze SA

Mathew,

Is what you did done on Image J or Weka?

Hi @RollTigs
The result is obtained using the above macro with ImageJ.
Please, what does “SA” mean (to analyze SA) ?
Weka is an ImageJ plug-in. (In fact of FIJI, variant of ImageJ)
I did it without using the PlugIn while @Alex.h used the plugin.
Weka is a more “powerful” tool.
Do you do this in an industrial or academic setting?

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Mathew,

SA= Surface Area
I do this in an academic setting, for graduate research work.

Thank you for all of the info

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You can use Set Measurement… and select Area.
Then Analyze Particles…
And you will have the area for all your ROI (this is what Mathew did in his macro)

run("Duplicate...", "title=mask ");
run("Convert to Mask");
run("Set Measurements...", "area add redirect=None decimal=2");
run("Analyze Particles...", "size=100-Infinity display exclude add");
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