Making substacks and concatenating them via MATLAB

Hi everyone!

I have a series of REC files that need to have their images reordered. I know how to do this via imagej (make substack and then concatenate) however I would like to make this an automated process whereby I can do a whole file of these files at once. I would prefer to do this via MATLAB. I am very new to this so any suggestions would be much appreciated!

Thank you!

Hi @FK7097,
I don’t fully get your question…do you need a way to make a substack with MATLAB?
Or do you need Fiji to make substack and then pass it to Maltab?

Could you please update somewhere some files/images as example to do some test?
Have a nice day,
Emanuele Martini

Any reason you need to use matlab instead of ImageJ?? Just curious. I use matlab as well for some tasks.

However it is hard to distribute and share matlab programs to non-matlab users. You can compile them, but the compiler is expensive. I also find it easier to distribute an ImageJ plugin rather than worry about creating a stand alone app.

I followed the example on stack overflow to make a stack.

test1=magic(10);
test2=ones(10);
teststack(:,:,1)=test1;
teststack(:,:,2)=test2;

size(teststack);

Hello,

Purely because I have more experience with MATLAB (I have next to none with ImageJ!).

If I can upload a REC file, make substacks (in this case using 1-16-4, 2-16-4, 3-16-4 and 4-16-4 as the images are ordered incorrectly in the original file) and then recombine them using concatenate and get ImageJ to automatically do this to several REC files (automatically uploading them from a file on my computer) that would be fantastic. I just don’t know how to do it!

Thanks for your help!

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