Radial averaging of 2-d tif image
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Kevin Wang
il 4 Feb 2016
Risposto: Sergey Loginov
il 5 Nov 2021
I am looking to compute a radial average of a 2-d tif microscopy image.
I want to start from a given pixel as the center, go progressively radially and record the intensities of all the pixels lying on the locus of the circle of that radius. Out of all these, I want to compute a graph of radius vs. Intensity.
Any ideas? I am looking to create a .m file to do this. Thank you!
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Image Analyst
il 4 Feb 2016
Modificato: Image Analyst
il 12 Set 2019
See my attached demo. Feel free to adapt, like to change the center or whatever. It gives the average radial profile within the blobs but you can use the same concept to do it over the whole image. The whole-image version is shown in the Answer below this one. Of course you could always just use ginput() to identify the center, compute the radiii, and use accumaray. Or just use a double for loop. So, there are several ways.
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Più risposte (3)
Image Analyst
il 4 Feb 2016
Modificato: Image Analyst
il 12 Set 2019
OK, so maybe that demo was too hard for you to adapt. Here is an easier, more straightforward demo using two for loops. It's easy to understand (as compared to accumarray which would probably be faster). See attached script below the image.
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Sergey Loginov
il 3 Nov 2021
Dear ImageAnalyst,
Thanks for mentioning accumarray function here! At image sizes greater than 1000x1000 it is much much faster than this circle drawing stuff!!
Regards
Hugo Trentesaux
il 7 Feb 2019
Modificato: Hugo Trentesaux
il 11 Set 2019
My version of the function :
function profile = radialAverage(IMG, cx, cy, w)
% computes the radial average of the image IMG around the cx,cy point
% w is the vector of radii starting from zero
[a,b] = size(IMG);
[Y, X] = meshgrid( (1:a)-cx, (1:b)-cy);
R = sqrt(X.^2 + Y.^2);
profile = [];
for i = w % radius of the circle
mask = (i-1<R & R<i+1); % smooth 1 px around the radius
values = (1-abs(R(mask)-i)) .* double(IMG(mask)); % smooth based on distance to ring
% values = IMG(mask); % without smooth
profile(end+1) = mean( values(:) );
end
end
3 Commenti
Sergey Loginov
il 3 Nov 2021
Dear Hugo,
I have seen your are have answered quite a lot o these questions about the radial profiles with the same code. I have myself implemented it in a similar manner recently. However it is really much much faster to use accumarray function from MatLab!!
Regards
SL
Sergey Loginov
il 5 Nov 2021
Using accumarray is indeed so much faster!
function [Tics,Average]=radial_profile(data,radial_step)
%main axii cpecified:
x=(1:size(data,2))-size(data,2)/2;
y=(1:size(data,1))-size(data,1)/2;
% coordinate grid:
[X,Y]=meshgrid(x,y);
% creating circular layers
Z_integer=round(abs(X+1i*Y)/radial_step)+1;
% % illustrating the principle:
% % figure;imagesc(Z_integer.*data)
% very fast MatLab calculations:
Tics=accumarray(Z_integer(:),abs(X(:)+1i*Y(:)),[],@mean);
Average=accumarray(Z_integer(:),data(:),[],@mean);
end
Sergey Loginov (2021). Very Fast Radial Profile (https://www.mathworks.com/matlabcentral/fileexchange/101480-very-fast-radial-profile), MATLAB Central File Exchange. Retrieved November 5, 2021.
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