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Threshold value question using otsu method

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I am doing Plant leaf disease detection & classification project. In that i am using otsu method to calculate threshold value for all leaves. But thershold value for some type of leaves could not detect the diseased part correctly..so i am using some constant threshold value(0.17,0.6). Can anyone please give some other method to find threshold value other than otsu method that is suitable for all type of leaves..

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Accepted Answer

Image Analyst
Image Analyst on 30 Dec 2014
See my attached code. I use an image with black background and even black spots inside it. I correctly identify the diseased areas and give the area fraction of them relative to the entire leaf area (diseased + healthy areas).
If this solves your question, please mark as Accepted.

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Asmalina Mohamed Saat
Asmalina Mohamed Saat on 19 Oct 2020
this is the original image (marine growth image), just like the leaf, i want the healthy(the part of image which no marine growth), and disease (the part of image which has marine growth)
this is the result by using your code
so from this histogram, how i want to separate the healthy and disease part?..
Image Analyst
Image Analyst on 19 Oct 2020
It looks like to me that the entire image has growth on it. Can you outline the parts you want to find, and say in words, what it is about those regions that indicates that there is growth there (like color or texture or whatever)?
And post this in your own, new question, not here in Packiya's 6 year old question.

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More Answers (6)

Sean de Wolski
Sean de Wolski on 24 Dec 2014
Show us an image! Without an image, it's very difficult if not impossible to guess at what you need.
Have you tried the multilevel otsu threshold? I.e. the Image Processing function imquantize?

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Packiya
Packiya on 30 Dec 2014
In the "black_background" both diseased part & the background part becomes white..so i could't say that the white part is a diseased part..but if i set the background as green i can point out the white part as a diseased part("green_background")..and i used that resultant image for further processing..in the next step i am splitting that resultant image into equal sized blocks.And then i counted the no. of blocks having either value 1(white)(background & healthy part-black) or value 0(black)(background & healthy part - white) in order to level the disease. so only i set the background as green.
Image Analyst
Image Analyst on 30 Dec 2014
No, that's not true. Or it's only true if you don't do it the way you're supposed to do it. With your way, you can't find the area of the leaf so you can't get area fractions.
First of all you segment for black. But you only want black if it's connected to the background, not if, say, there is a hole in the leaf due to disease, so you call imclearborder() and subtract that from the first binary image to get only the black connected to the border. Now mask your image and convert to hsv color space. Then define some hue sector that is "green" and sum the pixels in this sector - that's your green area. The rest of the pixels that aren't green and aren't part of the background are "disease". See my color segmentation routines, probably the HSV one would be best, in my File Exchange. Let me know if you need further help.
Spandan Tiwari
Spandan Tiwari on 15 Jan 2015
A clarification - the function to use for multilevel Otsu is multithresh . It outputs the threshold level(s). If required, the image can then be quantized using those thresholds using imquantize.

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Image Analyst
Image Analyst on 24 Dec 2014
I almost never use Otsu. It's usually no good. It's good mostly in cases with high contrast images with widely separated bimodal histograms, like where there is a uniform object on a uniform background and they have very different intensities. In real world situations, Otsu is often/usually not the best choice.
Actually using a fixed threshold like you're doing is a very good but under-used and under-appreciated method. People always want to use automatic thresholding but simple-minded autothresholding methods like Otsu have the drawback in that they always have to find a threshold somewhere in the histogram. Let's say you're looking at some image and the disease or stuff you want to find can be anywhere from 0% area fraction all the way up to 100% area fraction. Let's say you have a hump centered at 100 for good/normal/non-diseased pixels, and as the pixel goes "bad" the pixels get darker, which means their histogram shifts darker. Let's say one that was 100% bad would give you a hump at 50 gray levels. But what if you had a 100% bad image and Otsu would try to split that histogram and might give you something around 48 or 55 or whatever. It would give you the wrong area fraction because it was forced to find a threshold in a histogram hump that was essentially all the same - all bad. It would be much better to just say that anything below, say, 75 is bad and above 75 is good. That way you can get accurate area fractions all the way from 0% to 100%. If you have good control over your lighting and exposure so that similar images produce similar gray levels, then using a fixed threshold is a fine idea.
But in general, you need to decide upon a thresholding scheme based on the complete range of images that you expect to encounter. You haven't shown us even a single image, much less the entire span of images you expect the algorithm to be able to handle. Usually people asking for image processing advice attach an image to we don't have to work "blind."

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Sean de Wolski
Sean de Wolski on 24 Dec 2014
I agree that fixed thresholds are useful, especially for x-rays where the pixel values are a direct measure of energy passing through.
However, Otsu is appealing too for images where there is an object in the foreground and a background. It can do a good job dealing with changes in lighting etc.

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Anand
Anand on 15 Jan 2015
I haven't read the entire thread above. I'm sure there's a lot of good information there. I take it you are trying to threshold the 'diseased' portion of the leaf. So, essentially you want an image with disease pixels vs non-disease pixels.
I tried using the colorThresholder App with a couple of the images you've attached.
Here's how it looks:
im = imread('http://www.mathworks.com/matlabcentral/answers/uploaded_files/23137/Bacterial1.jpg');
% Open the colorThresholder
colorThresholder(im)
The hue channel in the HSV color space seems to separate the disease pretty well, so select HSV. Once the image opens in the HSV color space, move the hue slider appropriately to threshold the image.
Now export the code and use this on the other images.
Hope this helps!

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Packiya
Packiya on 23 Jan 2015
Thank u so much for your effort.

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gururaj moger
gururaj moger on 8 Apr 2016
how to check or detect the things instead of leaf and it must show it is not leaf

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Image Analyst
Image Analyst on 8 Apr 2016
Find the leaf and then invert the mask
nonGreenMask = ~greenMask;

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Raheel Rehman
Raheel Rehman on 7 Jan 2017
Can you please share the code?

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Image Analyst
Image Analyst on 7 Jan 2017
What code are you talking about? In my answer, I did post my code.

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tan aik hong
tan aik hong on 5 Oct 2018
thanks and it is very helpful for my project, but I had some problem, which is if the image of the leaf is healthy, through the code above, I had got the healthy region and diseases region. may I know is there any code that able to choose the image of leaf whether it is healthy or not. thanks

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Image Analyst
Image Analyst on 5 Oct 2018
No, that is the part that you need to do yourself, or hire someone to do. But once they've all been analyzed, and you have a boolean variable "isDiseased", then you can find the index of diseased ones, something like this
for k = 1 : length(isDiseased)
if ~isDiseased
continue; % Skip healthy ones.
end
thisFileName = allFileNames{k};
imshow(thisFileName);
drawnow;
end

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