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How can I get the correct output using the Auto threshold imagej Plugin?

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Alaa
Alaa on 28 Feb 2016
Commented: Walter Roberson on 29 Feb 2016
Hi every one, I have tried the following code, where I read an image from a directory and use ImageJ Auto Threshold plugin to segment my image. Any one can do that easily using imagej program as follow:
1- Open an image.
2- Then Go to : image->Adjust->Auto Threshold.
3- From methods drop list: Select the mean method.
4- Pick the white object on the black background.
My problem is I can't call this plugin correctly from Matlab. My Matlab code as follows:
javaaddpath 'C:\Program Files\MATLAB\R2013b\java\mij.jar'
javaaddpath 'C:\Program Files\MATLAB\R2013b\java\ij.jar'
MIJ.start
MIJ.run('Open...', 'path=[E:\\sun\\Endothelium Project\\Endothelium Code\\MIJ Code\\ENDOTHELIAL IMAGES\\12.bmp]');
MIJ.run('Threshold...','setAutoThreshold=mean');
MIJ.run('setOption=BlackBackground');
MIJ.run('Convert to Mask');
SegmentedImage = (VorImage);
figure, imshow(SegmentedImage);
Thank you in advance.

  1 Comment

Walter Roberson
Walter Roberson on 29 Feb 2016
Your line
SegmentedImage = (VorImage);
is suspicious. If you are attempting to retrieve data from MIJ then you would need a reference to MIJ there. For example it might look something like
SegmentedImage = MIJ.VorImage;

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