MATLAB Answers

Setting certain pixels in a grayscale image to RGB (red) for MIP

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Alex G
Alex G on 6 Aug 2018
Edited: Thorsten on 9 Aug 2018
Hey again. I have a grayscale image and would like to highlight certain pixels by setting them to red, e.g.
save_array = image;
save_array(Omega==1) = %RED
Is there an easy way to do this? I will be taking the image (3D array), calculating the MIP (max intensity projection) by
mip_final = max(save_array, [], 3);
and would then like the red pixels to appear on the MIP (2D). So if a pixel is red anywhere in the z-dimension, it will appear red in the 2D MIP


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Answers (2)

Image Analyst
Image Analyst on 6 Aug 2018
Try this:
redChannel = grayImage; % Initialize
greenChannel = grayImage; % Initialize channel for green and blue channel.
redChannel(Omega) = 255;
greenChannel(Omega) = 0;
rgbImage = cat(3, redChannel, greenChannel, greenChannel);


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Alex G
Alex G on 7 Aug 2018
Of course, I'll try to get something to you soon. I'll try to explain it now though:
We have a 3D grayscale array in matlab. We have a binary array Omega of the same dimensions. I would like to make a MIP of that grayscale array, but whenever Omega is true in the xy-plane (irrespective of z), I would like the corresponding pixel to be red
...from writing this I guess I could take a MIP of the image, a MIP of Omega, and where Omega's MIP is true would be red in the final MIP?
Image Analyst
Image Analyst on 7 Aug 2018
OK, so you have a volumetric image, like from CT or MRI. So just mask the image
masked3DImage = grayImage3d; % Initialize
masked3DImage(~Omega) = -inf; % Mask
masked3DImage = max(masked3DImage , [], 3); % Do MIP
masked3DImage(~Omega) = 0; % minus infinity set to zero or whatever value you want outside of the mask.
Alex G
Alex G on 7 Aug 2018
This looks great. Also this might sound stupid, but where do I set the selected voxels to red (that's the issue I'm trying to resolve)? As a reminder, (Omega == 1) are the selected voxels
I believe I can just run masked3DImage through your first comment's code?
Thanks again.
P.S. I'm getting a "Attempt to grow array along ambiguous dimension" error. Probably because we reference Omega after making it a MIP. The MIP is 2D and Omega is 3D, so perhaps this is an issue?

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Thorsten on 8 Aug 2018
From the above discussion, I came up with this solution:
% fake some data
X = rand(10, 10, 23);
N = prod(size(X));
idx = randi(N, 1, round(0.01*N)); % 1% of all pixels are 1
X(idx) = 1;
Omega = X == 1; % find the values that are 1 in X
idx = sum(Omega, 3) > 0; % project to a 2D binary image
MIP = max(X, [], 3);
% create a color image from MIP
R = MIP; R(idx) = 1;
G = MIP; G(idx) = 0;
B = MIP; B(idx) = 0;
I = cat(3, R, G, B);


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Image Analyst
Image Analyst on 9 Aug 2018
Yes, of course it does, because the other pixels are opaque. For true volume visualization, you can't use MATLAB, which is limited to isosurfaces and cutaway views last I checked. You'll need to use a true volume visualization program like Avizo.
Alex G
Alex G on 9 Aug 2018
Thanks for the advice, I'll try out Avizo and see if my PI can get it for the lab. I do see your point - even if we increase transparency, it'll be difficult to see the voxels at the center of any 3D volume when viewed in 2D.
I realized I need to implement a density-weighted approach to my adaptive sampling, so hopefully the MIP visualization will work better after that :) I'm sure my PI doesn't want to pay for another license
Thorsten on 9 Aug 2018
You can visualize only the red blocks using plotcube from the FileExchange:
X = rand(10, 10, 23);
% X = rand(3000,1000,600);
N = prod(size(X));
idx = randi(N, 1, round(0.01*N)); % 1% of all pixels are 1
X(idx) = 1;
[x, y, z] = ind2sub(size(X), idx);
for i = 1:numel(x)
plotcube([1, 1, 1], [x(i) y(i) z(i)], .8, 'r')
if i == 1, hold on, end
axis equal
grid on

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