Image Processing: DeInterleaving, is it possible?

Hello!

Is it possible for MatLab to "De-Interleave" stacked images? Originally this is a ImageJ plugin function, but it would be very useful it can be run through MatLab.

Thanks!

-Frank

Website

http://www.macbiophotonics.ca/imagej/stack.htm

Diagram

[Frank]

I'm aiming for getting images De-Interleaved and saved into a different folder through a loop function

Answer 1

[Sean de Wolski]

Copied from Andrew with modifications:

function [A, B] = deinterleave(file_name)
   I  = imread(file_name); %don't call a variable image since it overwrites built-in function.

   A = I(:,:,1:2:end);
   B = I(:,:,2:2:end);

Not only is this vectorized but it can account for volumes with an odd number of pages (slices).

You could also change it to accept a 3D volume rather than a file name; I recommend that.

function [A, B] = deinterleave(I)
%I is a 3D volume
 A = I(:,:,1:2:end);
 B = I(:,:,2:2:end);

[Frank]

I've tried this and i'm not sure how to interpret what I received.

It returned a lot of numbers and columns.

Code:

function [A, B] = deinterleave(file_name);

I = imread('343b001.tif');

A = I(:,:,1:2:end);

B = I(:,:,2:2:end);

function [A, B] = deinterleave(file_name);

I = imread('343b001.tif');

A = I(:,:,1:2:end);

B = I(:,:,2:2:end);

[Sean de Wolski]

Does 343b001.tif contain a 3-d image?

Did you put a semicolon after the call?

call it from the command line with:

[A B] = deinterleave('343b001.tif');

and use this as the function. Don't change file_name to the one instance string.

function [A, B] = deinterleave(file_name)

I = imread(file_name); %don't call a variable image since it overwrites built-in function.

A = I(:,:,1:2:end);

B = I(:,:,2:2:end);

[Frank]

So I would use:

function [A, B] = deinterleave(file_name);

I = imread('file_name');

A = I(:,:,1:2:end);

B = I(:,:,2:2:end);

Do you mean variable image as in an image stored to a variable?

[Sean de Wolski]

NO!!!

'filename' is a string. Unless you have a file named 'filename' with no extension it will fail. filename is a variable that contains a string (in this case passed in as '343b001.tif'.

Literally copy and paste these four lines and store it in deinterleave.m

function [A, B] = deinterleave(file_name)

I = imread(file_name); %don't call a variable image since it overwrites built-in function.

A = I(:,:,1:2:end);

B = I(:,:,2:2:end);

Then call it (from the command line) with

[A B] = deinterleave('343b001.tif');

[Frank]

Okay

I got an error, but when I called it with

"[A B] = deinterleave('343b001.tif'); "

it ran.

I only have an image stored in A

Would the images split between A and B?

[Frank]

Error:

??? Input argument "file_name" is undefined.

[Sean de Wolski]

One 2d image? Or is it 3D?

What does

size(A)

return

What does:

size(imread('343b001.tif'))

return?

[Frank]

The image is 2-d, i'll post it above.

size(A) returned: 256 64

size(imread('343b001.tif') returned 256 64

[Sean de Wolski]

Well then how to do you plan on deinterleaving it? There are no slices to deinterleave!

[Frank]

Did you use the posted image? I think it may have changed it, that or I've uploaded the wrong image. Let me re-upload.

[Sean de Wolski]

No. Your definition of interleaving presented above requires a 3d image. You don't have a 3d image right now so this whole objective is ill-posed.

[Frank]

The function of deinterleaving organizes image stacks in the diagram above, it doesn't require the images to be in 3d, otherwise how was I able to deinterleave 2d images.

Thanks for the help though

[Sean de Wolski]

Yes it does require them to be 3D. How can you pull the second slice from a 2d image? ImageJ may work differently and be able to read a file full of 2d images, but it's viewing that file internally as a 3D image.

Answer 2

[Andrew Fowler]

This should be fairly straightforward if you are already working with a format that can be easily imported into matlab as an array. If you're working with a standard image format like .tif, or even dicom files, you should be able to set up an easy function with a quick for loop. Here's an example for a dicom file:

function [A, B] = deinterleave(dicom_filename)

image  = dicomread(dicom_filename);
height = length(image(:,1,1));
width  = length(image(1,:,1));
slices = length(image(1,1,:));

A = zeros(height, width, slices/2);
B = A;

for i = 1:length(image(1,1,:)
A(:,:,i) = image(:,:,(2*i-1));
B(:,:,i) = image(:,:,(2*i));
end

You can use IMREAD instead of DICOMREAD if you're using another format. If you're using a more esoteric image format like REC-PAR or 2dseq, you may need to do a little more work to actually import your images into matlab as arrays.

[Frank]

I am working with .tif images, so would I simply input the name of the file to the function?

Like:

function [A, B] = deinterleave('name.tif');

image = dicoread('name.tif');

...

[Andrew Fowler]

you should use IMREAD instead of DICOMREAD. Also Sean has some really good additions that you should probably follow. Ex:

i = imread('name.tif')

[Frank]

Thanks for the help