Saving an array of images as an 'Image Stack'

Hi.

I obtain grayscale image' 'img' that I add to a 'stack' i.e. image array by:

imgArray{index}=img

So If I have say 5 images in the imgArray, I have been saving them to disk by writing them out individually as tifs via:

prefix=get(handles.editSaveName,'String');

for k=1:5     
    imwrite(imgArray{k},sprintf('%s\\%s%04d.tif',folder,prefix,k));    
end

BUT, I want the option to say the array of images as a single file i.e. an image stack. I thought the following would do it

try
 imwrite(imgArray,sprintf('%s\\%s.stk',folder,prefix));   
catch
  h = errordlg('Error Saving Image STK')  
end

But it always fails. Is there an obvious error?

Thanks

Jason

[Walter Roberson]

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

Answer 1

[Jan]

According to the matlab documentation you can store multiple images to a single file as follows:

imwrite(im1,'myMultipageFile.tif')
imwrite(im2,'myMultipageFile.tif','WriteMode','append')

See https://www.mathworks.com/help/matlab/ref/imwrite.html --> Write Multiple Images to TIFF File.

[Jason]

Why does the following not work

for k=1:5     
    imgArray3(:,:,k)=imgArray{k};    
end  

 imwrite(imgArray3,sprintf('%s\\%s.stk',folder,prefix));

[Jan]

What error are you getting? On my Matlab version, the stk format is not supported.

[Jason]

I assumed you could use what ever extension name you wanted to. The code is testing on a compiled version using the MRC so i cannot get to the error message

[Adam]

imwrite uses the extension to work out the format in which to save the file.

[Jason]

I see there is a fmt optionwith imwrite to set the type as either tif or tiff. It still doesn't seem to work - so its seems I must have the .tif or .tiff extension. I really wanted a different extension to distinguish this file as a lot of tiffs rather than just a single tiff

[Jason]

Correction. It should be possible to save the tiffs using any extension using fmt option

imwrite(___,fmt) writes the image in the format specified by fmt, regardless of the file extension in filename. You can specify fmt after the input arguments in any of the previous syntaxes.

[Joe Sheppard]

I have seen 'WriteMode' 'append' suggested everywhere, but for some reason MatLab still saves the files as seperate tiffs rather than a single file, why would this be?

[Sai Sirish Gokavarapu]

Hey there! Even I'm trying to use to convert a .avi file to a .tif STACk but unfortunately the code just converts it to a set of .tif images despite using 'WriteMode' and "append".

Here's the code, it's similar to that of Joe.

%% To convert avi files to tif images
obj = VideoReader('video.avi');
vid = read(obj);
frames = obj.NumberOfFrames;

% This just converts them to a set of images
% for x = 1 : frames
%     imwrite(vid(:,:,:,x),strcat('frame-',num2str(x),'.tif'));
% end

%This is meant to amend that and to make a .tif stack
for x = 1 : frames
        imwrite(vid(:,:,:,x),strcat('frame-',num2str(x),'.tif'), 'Compression', 'none','WriteMode', "append");
end

[Lili Xu]

I've been dealing with the same issue the brutal way by just saving the separate tifs in the same folder and open the folder using ImageJ afterwards and let ImageJ do the job of combining the separate tifs into a stack...

[Yael Grossman]

@Lili Xu@Sai Sirish Gokavarapu The bug in the code is that you're chaning the file name for each iteration

for x = 1 : frames
        imwrite(vid(:,:,:,x),'All_frames.tif', 'Compression', 'none','WriteMode', "append");
end

[Cody Crosby]

Thank you Yael! That worked perfectly for me.