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kmader/Download and Setup

Last active August 29, 2015 13:57
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Exercise 4 Setup and K-Means Code
Raw
Download and Setup
% change to your home directory
cd('~')
% download and extract the latest version of fiji
unzip('http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip','./')
% add the Fiji scripts folder to the matlab path
addpath 'Fiji.app/scripts'
% start Miji
Miji
% for some reason Miji changes to directory so go back to the home directory
cd('~')
% to test if it works
% Miji_Test
Raw
Run K-Means
MIJ.run('Embryos (42K)');
imData = double(MIJ.getCurrentImage);
% raster scan image to 3 , 1D arrays
imList=reshape(imData,[],3);
% peform k-means
[groupList,centers]=kmeans(imList,3);
% reshape into an image
groupIm=reshape(groupList,size(imData,1),size(imData,2));
% show the result
imagesc(groupIm);
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kmader commented Mar 12, 2014

curl does not work on these matlab versions because of library issues

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