Masking images/matrixes

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$Amit Ifrach$

Amit Ifrach 2023-7-14

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1995973-masking-images-matrixes

评论： Image Analyst 2023-7-18

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לק"י

Hello!

I got an image of some stained cells:

And I have a grayscale mask such as this:

(different shades are covering different cells as you can see).

I want to systematically go through each gray shade in the mask and to extract (or leave) the area in the cells image.

I looked up for a quick command, but haven't found one.

I tried to use find command, but I get vectors as a result and can't use it to "talk" with the original image matrix.

This is the code I'm using:

img=imread("4.7.23 ut cd4_prfrn acd3+11002c3.tif");
mask=imread("4.7.23 ut cd4_prfrn acd3+11002c3_cp_masks.png");
i=max(max(mask))
maskx=[];
masky=[];
[maskx, masky]=find(mask==i);
imgmasked=img(maskxy,masky)

(I'm using a for loop to go through all indexes, but it will come later, I want to succeed masking right now)

What is the right way to handle this problem please?

Thanks,

Amit.

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Jon 2023-7-14

Please attach your two files

$Amit Ifrach$

Amit Ifrach 2023-7-15

לק"י

Hi jon,

I added them. The cell's picture was converted from TIF to png.

Thanks!

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Answer 1

Image Analyst 2023-7-14

1
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https://ww2.mathworks.cn/matlabcentral/answers/1995973-masking-images-matrixes#answer_1273283

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It looks like your mask is actually a labeled image since each blob seems to have a unique value (label). So in that case to get the area of each labeled blob you'd simply do

props = regionprops(labeledImage, 'Area');
allAreas = [props.Area] % Will give a vector of 5 areas.

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$Amit Ifrach$

Amit Ifrach 2023-7-15

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לק"י

Hi Image analyst, thanks for the answer!

I don't need the area of each mask. I want to mask out from the original cell image the exact area found in each mask.

I'll try to ask it more clearly:

I have grayscale image of masks. each gray color represents a cell.

First I want to take the mask image and leave it only with one cell area mask. that means, if the range of intensities of the mask image is 5 (as in the example mask image), I want to zero out all values, except the value 1 for example, or 2, or 3 etc. I want to be left with only spefic value in the mask and zero all the rest.

It should look something like this:

[1 0 0 2 0
 3 0 5 0 0
 4 0 0 0 0]   %--zero all values except the value 4 for example--->    

[0 0 0 0 0
 0 0 0 0 0
 4 0 0 0 0] 

Then I want to take this mask and zero out all the values in the cell's image according to mask.

It should go like this:

[25 3 14 8 0
 2 24 0 0 0
 65 12 73 72 0] %--zero all values except the pixel in the position corresponding to value 4 for in the zeroed mask---> 

[0 0 0 0 0
 0 0 0 0 0
 4 0 0 0 0] %the zeroed mask I want to multiply/mask out by.

[0 0 0 0 0
 0 0 0 0 0
 65 0 0 0 0]

I hope I managed to explain myself better.

I know realize the last stage is just matrix multiplication. The first stage allways result in vectors (when using find command or other commadns).

Thanks,

Amit.

Matt J 2023-7-18

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Yes,

imgthldtmp=zeros(size(imgmask));
thldfnd= imgfltrd>(thldmltplr(k)*pxllstavg);
imgthldtmp(thldfnd)=imgfltrd(thldfnd);

Image Analyst 2023-7-18

Heck no. Shorter would be even more cryptic and hard to follow than it is now. No comments, cryptic variable names, etc. I don't know what you did but whatever, if it works for you, fine.

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