How to show Tiff stacks

Hi everyone;

I'm trying to show a tiff stack '57 images as one file' but I faced this problem:

 Warning: Can only display one frame from this multiframe file:

"Stack.tif".

> In imuitools\private\getImageFromFile at 20

In imuitools\private\imageDisplayParseInputs at 74

In imshow at 198

In Prg at 4

how can I display a tiff stack image? and after I applied some processes how can I collect them again 'refile them'

Answer 1

[Jeff E]

You can read each tiff image in one at a time using imread (note I'm making some assumptions...like you do indeed have a multipage tiff):

tiff_info = imfinfo('2-A^11815^52071.tif'); % return tiff structure, one element per image
tiff_stack = imread('2-A^11815^52071.tif', 1) ; % read in first image
%concatenate each successive tiff to tiff_stack
for ii = 2 : size(tiff_info, 1)
    temp_tiff = imread('2-A^11815^52071.tif', ii);
    tiff_stack = cat(3 , tiff_stack, temp_tiff);
end

And you can then use the 'append' switch to write each tiff as a new image in a multi-page tiff:

%write a Tiff file, appending each image as a new page
for ii = 1 : size(tiff_stack, 3)
    imwrite(tiff_stack(:,:,ii) , 'new_stack.tif' , 'WriteMode' , 'append') ;
end

[Soum]

Thank you a lot for the excellent answer but if I have a separate tiff

images and I would to read them as one tiff file can I do it?

Many thanks in advance

[Jeff E]

If you mean separate tiff files, all in one directory, then change the first bit of code to use the output from DIR (again, assuming you have more than one tiff in a directory):

files = dir('C:\temp\*.tiff');
tiff_stack = imread(files(1).name);
for ii = 2 : size(files, 1)
    temp_tiff = imread(files(ii).name);
    tiff_stack = cat(3 , tiff_stack, temp_tiff);
end

If you meant something else, please elaborate.

[Soum]

thank you but I mean I've a 57 images .tiff 'separated' and I wanna read

them as one multipage tiff image

Answer 2

[Shep Bryan]

In my case it ends up being a couple orders of magnitude faster to avoid using imread. Try:

function data = FastTiff(filename)

warning('off','all') % Suppress all the tiff warnings

tstack  = Tiff(filename);

[I,J] = size(tstack.read());
K = length(imfinfo(filename));

data = zeros(I,J,K);
data(:,:,1)  = tstack.read();
for n = 2:K
    tstack.nextDirectory()
    data(:,:,n) = tstack.read();
end

warning('on','all')

end

Notice that I suppress the warnings in my code because the format of my data is strange.

Answer 3

[Ashish Uthama]

It would help to clarify the nature of your input files (Folder of tiffs? One tiff file with multiple IFD/s? Or one tiff file with ImageJ style stack?)

You could look at tiffreadvolume to read in the latter two types. And explore volshow and volumeViewer if its 3D data, or just implay if its a time series.

For stream processing, you could also explore blockedImage to read+process+write large 3D data from tiff files.