image sequence Tif files to stack, switch channels to frame

Hello all,

I have a series of tif files which are the image sequence from microscopy movie. I managed to use Tiff function to export them as a stack.

When I used ImageJ to check the properties of the stack, what I got is 74 channels (c), instead I want to get a stack has 74 frames (t).

I attach my code how to stack the image sequence here

% Images to Stacks 

imagefiles = dir('*.tif');      
nfiles = length(imagefiles);    % Number of files found

a = 0;
b = 0;
for ii=1:nfiles
    inf = imfinfo(imagefiles(ii).name);
    a=max([a, inf.Height]);
    b=max([b, inf.Width]);
end

tagstruct.ImageLength = a;
tagstruct.ImageWidth = b;

tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
tagstruct.BitsPerSample = 16;
tagstruct.SamplesPerPixel = 1;
tagstruct.RowsPerStrip = 1;
tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
tagstruct.Software = 'MATLAB';

t = Tiff('Test.tif','a');
setTag(t,tagstruct)


for ii=1:nfiles
   temp=uint16(zeros(a,b));
   currentfilename = imagefiles(ii).name;
   currentimage = imread(currentfilename);
   temp(1:size(currentimage,1),1:size(currentimage,2),ii)=currentimage;

  
   write(t,temp(:,:,ii));
   writeDirectory(t);
   setTag(t,tagstruct)
end 

close(t)

My guess would be changing parameters in tagstruct could swich the channal and frame, but I don't know exactly how.

If anyone has an idea about how to do it, it will be so helpful.

Thank you in advance!

[Walter Roberson]

ImageJ uses some private TIFF tags to signal that the TIFF is an ImageJ stack.

https://www.mathworks.com/matlabcentral/answers/282397-writing-multidimensional-tiff-files-using-imwrite#answer_220660

[Yunwei]

Hi,

Thanks for the reply.

does it mean that I can only change the stack dimention when i can open ImageJ in MATLAB?

Is there any way to solve it within Matlab?

Answer 1

[Dheeraj]

Hi,

I understand that you are trying to find ways to convert channels in your tiff file to frames. The reason why ImageJ shows 74 channels (c) instead of 74 frames (t) in your stack is because by default, ImageJ imports TIF stacks as channels instead of frames.

It is possible to change how ImageJ imports TIFF stacks so that they are imported as frames instead of channels. To do this, you can use the following steps:

1. Open your multi-channel TIFF stack in ImageJ.
2. Go to "Image" in the menu bar.
3. Select "Hyperstacks" and then choose "Stack to Hyperstack."
4. In the "Stack to Hyperstack" dialog box that appears, you can specify how you want to reorganize your channels into frames. You'll need to provide the following information:
5. Ensure that "Use 1 for dimension not used" is selected for the other dimensions that you are not changing (e.g., time, slices, and channels).
6. Click "OK" to convert your stack into a hyperstack with channels reorganized into frames.

Hope this helps!