matlab: texture classification - image

I have a histology image like this:
From the image, we can observe there are two kinds of different cells.
and
Is there any way that I can separate these two types of cells into two groups?

How about using your raw image and previous code to achieve this?
% % % your old code
I=imread(file);
t1=graythresh(I);
k1=im2bw(I,t1);
k1=~k1;
se = strel('disk',1);
k0=imfill(~k1,'holes');
cc = conncomp(k0);
k0(cc.PixelIdxList{1})=0;
k1=imfill(k1,'holes');
mask=k0 | k1;
%%%%%%%%%%%%%%%%%%
This will give you:
I=rgb2hsv(I);
I=double(I);
I1=I(:,:,1); % again, the channel that can maximizing the margin between donut and full circle
Imask=(I1-0.2).*(I1-0.9)<0;
k2=mask-Imask;
k2=bwareaopen(k2,100);
This will give you:
k2=mask-Imask;
I2=zeros(size(I1,1),size(I1,2),3);
I2(:,:,1)=(k2==1)*255;
I2(:,:,3)=((I1-0.2).*(I1-0.9)<0)*255;
imshow(I2)
will finally give you (the two types are stored in two channels in the rgb image):

I would use regionprops
props=regionprops(YourBinaryImage, 'Solidity');
The objects with a high solidity will be the disks, those with a lower solidity will be the circles.
(Edit) More formally:
I=imread('yourimage.jpg');
Bw=~im2bw(I, 0.5);
BWnobord = imclearborder(Bw, 4); % clears the partial objects
Props=regionprops(BWnobord, 'All');
solidity=cell2mat({Props.Solidity});
Images={Props.Image};
Access the elements of Images where the value in solidity is higher than 0.9 and you get your disks. The circles are the other ones.
Hope it helps

Related

How to Draw BoundingBox or Tag Objects Which Has Less Area Than Others

In my image I have 5 Objects in black-white form. Some are respectively small, some are bigger.
So what i am trying to do is drawing a BoundingBox or tag the objects which has less area than others (ex. under 10pixels/area) .
I couldn't make this happen, can anyone help?
That's two separate problems. The first is to select only objects above a certain area. So simply remove all objects below it:
clean = bwareaopen (im, 10); # remove all objects with area below 10
Then for the second problem there are many possibilities. You can get their borders:
borders = bwperim (clean);
imshow (borders);
You can label them:
labeled = bwlabel (clean);
imshow (labeled);
Or you can get their bounding box (which depending on the shape of your objects may overlap):
props = regionprops (clean, 'BoundingBox');
all_bb = props.BoundingBox;
boxes = false (size (clean));
for i = 1:numel (all_bb)
bb = all_bb{i};
bb(round (bb(2):bb(2)+bb(4), bb(1):bb(1)+bb(3))) = true;
end
imshow (boxes);
Note: this was written out of my head, no testing. There may be small oversights, but nothing major.

segment object(leaf) which is on the white paper using image processing

I want to get only leaf from an image.
The background is a normal white paper(A4) and there is some shadow.
I apply some method (structure element,edge detection using filter) but I cannot find the general way which can apply all the image.
these are examples.
Are there better methods for this problem??
thank you
another example.
and the result I got is
By using
hsv_I = rgb2hsv(I);
Is = hsv_I(:,:,2);
Is_d = imdilate(Is,strel('diamond',4));
Is_e = imerode(Is,strel('diamond',2));
Is_de = imerode(Is_d,strel('disk',2));
Is_def = imfill(Is_de,'holes');
Is_defe = imerode(Is_def,strel('disk',5));
Then Is_defe is a mask to segment
But the method that i did is very specific. I cannot use this in general.
If you have the Image Processing Toolbox, you could do as follows:
The code below first estimates the threshold with the function graythresh, thresholds the image and fills holes with the imfill function. Suppose I is a cell containing your RGB images:
for k=1:length(I)
t=graythresh(rgb2gray(I{k}));
BW{k}=imfill(~im2bw(I{k}, t), 'holes');
subplot(length(I),1,k), imshow(BW{k});
end

Add the three channels in a image to obtain a color image MATLAB

I am modifying images in matlab and I have a problem.
I need to separate the 3 channels of color and modify them separately.
I use this to obtain the three channels:
a = imread('./images/penguins.png');
colorlist = {'R','G','B'};
subplot(2,2,1);
imshow(a);
for k=1:3
subplot(2,2,k+1);
imshow( a(:,:,k));
title(colorlist{k});
end
a(:,:,k) is one color of the three. The problem is when I add the three vectors in one, to obtain the color image. I do this:
A=a(:,:,1)+a(:,:,2)+a(:,:,3)
figure; imshow(A);
But it dont works, it only show me a very highlight image, no a color image.
Anyone knows how can I recover the color image? Thanks for yout help^^
You are adding the values of the three layers instead of concatenating them in a 3D array.
Try this:
A= cat(3, a(:,:,1), a(:,:,2), a(:,:,3));
I should also note that you can edit the layers simply by indexing, say you want to switch the red and green components:
I1 = imread('http://i.stack.imgur.com/1KyJA.jpg');
I2=I1;
I2(:,:,1)=I1(:,:,2);
I2(:,:,2)=I1(:,:,1);
imshowpair(I1,I2, 'montage');
Now if I take your title literally, let's say you do want to add the three layers and display the result with a colormap, you can do:
A=a(:,:,1)+a(:,:,2)+a(:,:,3)
imagesc(A); axis image;
colorbar;
Results:

Cubism.js / d3.js Scale and Extent

Can someone provide some insight on how scales and extents work together in cubism.js
.call(context.horizon()
.extent([-100, 100])
.scale(d3.scale.linear().domain([-10,10]).range([-100,100])
)
);
For example what does the code above do? If the values are generated using a random number generator (numbers between -10 and 10)
I know extent is used to set the maximum and minimum.
I know how to define a scale, example:
var scale = d3.scale.threshold().domain([100]).range([0,100])
console.log(scale(1)) // returns 0
console.log(scale(99.9)) // returns 0
console.log(scale(88.9)) // returns 0
console.log(scale(100)) // returns 100
I read about d3.scales here http://alignedleft.com/tutorials/d3/scales/
My main issue is that I want to define thresholds for my data, very simple
0-98 Red
98-100 Pink
100 Blue
Or maybe just
0-99.99 Red
100 Blue
But I'm not being able to use all what I've read to construct something that works.
I'm guessing that you just want to use a different color to represent anomalies in your data. If that is true, you don't need to create a domain and range.
You can just create a custom color palette like this:
var custom_colors = ['#ef3b2c', '#084594', '#2171b5', '#4292c6', '#6baed6', '#9ecae1', '#c6dbef', '#deebf7', '#f7fbff', '#f7fcf5', '#e5f5e0', '#c7e9c0', '#a1d99b', '#74c476', '#41ab5d', '#238b45', '#006d2c', '#00441b'];
This color palette was constructed using the palette on this page with an extra red color tacked on to the end.
Then just call the custom colors like this:
d3.select("#testdiv")
.selectAll(".horizon")
...
.call(context.horizon()
.colors(custom_colors)
));
Play around with the colors until you find a combination that you like. In this above example, only the outlier will be in red while the rest will follow the blue and green pattern.
Hope this helps!

adjusting row height in R image() function

I'm drawing several heatmaps using the image() function in R.
The sizes of the heatmaps are quite variable, so every heatmap has a different height, however I want the row heights be uniform across heatmaps.
So I create heatmaps from these two matrices, and the heights of each cell are different between two heatmaps:
m1<-replicate(40, rnorm(20))
image(1:ncol(m1), 1:nrow(m1), t(m1), axes = FALSE,xlab="",ylab="")
m2<-replicate(40, rnorm(10))
image(1:ncol(m2), 1:nrow(m2), t(m2), axes = FALSE,xlab="",ylab="")
For the life of me, I can't figure out how can I specify the row height. It must be a very easy fix, but I can't figure it out.
You give very limited information. E.g., do you want to create PDFs? Or place several plots on one page?
Here is one solution:
par(fin=c(5,5),mar=c(0,0,0,0))
image(1:ncol(m1), 1:nrow(m1), t(m1), axes = FALSE,xlab="",ylab="")
par(fin=c(5,2.5),mar=c(0,0,0,0))
image(1:ncol(m2), 1:nrow(m2), t(m2), axes = FALSE,xlab="",ylab="")
I am sure there are more elegant solutions depending on what you actually want to do with the graphs.
Just set a common maximum number of rows for all the heatmaps using the ylim parameter:
m1<-replicate(40, rnorm(20))
m2<-replicate(40, rnorm(10))
image(1:ncol(m1), 1:nrow(m1), t(m1), axes=FALSE, ann=FALSE, ylim=c(0, max(sapply(list(m1,m2),nrow)) ))
image(1:ncol(m2), 1:nrow(m2), t(m2), axes=FALSE, ann=FALSE, ylim=c(0, max(sapply(list(m1,m2),nrow)) ))
You may want to manually specify the ylim argument and have that be the same between the 2 plots:
par(mfrow=c(1,2))
image( 0:ncol(m1), 0:nrow(m1), t(m1), axes=FALSE, xlab='', ylab='',
ylim=c(0,nrow(m1)) )
image( 0:ncol(m2), 0:nrow(m2), t(m2), axes=FALSE, xlab='', ylab='',
ylim=c(0,nrow(m1)) )

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