Writing tiff file with multi channel and slices

Hello,

I would like to make a tiff file with c=2, z=10, t=1. Input array is 4 dimension, [height, width, channel, slice]. Currently I am using the code below, however, the output tiff file becomes c=1, z=20, t=1. Can anybody help me to fix it?

function write3Dtiff_Slice(array, filename)
dims = size(array);
% Ensure the array has four dimensions
if length(dims) < 4
    dims(end+1:4) = 1;
end
% Set data type specific fields
if isa(array, 'single')
    bitsPerSample = 32;
    sampleFormat = Tiff.SampleFormat.IEEEFP;
elseif isa(array, 'uint16')
    bitsPerSample = 16;
    sampleFormat = Tiff.SampleFormat.UInt;
elseif isa(array, 'uint8')
    bitsPerSample = 8;
    sampleFormat = Tiff.SampleFormat.UInt;
else
    disp('Unsupported data type');
    return;
end
% Loop through slices
for s = 1:dims(4)
    % Open TIFF file for each slice in append mode
    outtiff = Tiff(filename, 'a');
    % Loop through channels for the current slice
    for c = 1:dims(3)
        % Set tag structure for each channel of each slice
        tagstruct.ImageLength = dims(1);
        tagstruct.ImageWidth = dims(2);
        tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
        tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
        tagstruct.SamplesPerPixel = 1;
        tagstruct.BitsPerSample = bitsPerSample;
        tagstruct.SampleFormat = sampleFormat;
        % Set the tag for the current channel
        outtiff.setTag(tagstruct);
        % Write the channel data
        outtiff.write(array(:,:,c,s));
        % Create a new directory for the next channel unless it's the last channel of the last slice
        if c ~= dims(3) || s ~= dims(4)
            outtiff.writeDirectory();
        end
    end
    % Close the file for the current slice
    outtiff.close();
end
end

Answer 1

[DGM]

It's doing exactly what you're telling it to do. You have a stack of size [H W C F]. You're splitting the stack into C*F individual single-channel images. If that's not what you want, then what do you want?

This writes a set of 2-channel frames instead of a bunch of loose channels.

fname = 'fname.tif';

% a MxNx2x5 4D image
inpict = imread('peppers.png');
inpict = repmat(inpict(:,:,1:2),[1 1 1 5]);

% create the file
write3Dtiff_Slice(inpict,fname)

% get the information in the multitiff image
info = imfinfo(fname);
nframes = numel(info);

% read images to check that it's the expected size
% this assumes all the frames are the same class and size
C(:,:,:,1) = imread(fname,1);
C = repmat(C,[1 1 1 nframes]);
for f = 2:nframes
    C(:,:,:,f) = imread(fname,f);
end

% test it
size(C) % the size is as expected

ans = 1×4

384 512 2 5

isequal(C,inpict) % it's the same as the original

ans = logical
   1

function write3Dtiff_Slice(array, filename)
dims = size(array);

% Ensure the array has four dimensions
if length(dims) < 4
    dims(end+1:4) = 1;
end

% Set data type specific fields
if isa(array, 'single')
    bitsPerSample = 32;
    sampleFormat = Tiff.SampleFormat.IEEEFP;
elseif isa(array, 'uint16')
    bitsPerSample = 16;
    sampleFormat = Tiff.SampleFormat.UInt;
elseif isa(array, 'uint8')
    bitsPerSample = 8;
    sampleFormat = Tiff.SampleFormat.UInt;
else
    disp('Unsupported data type');
    return;
end

% Open TIFF file for each slice in append mode
outtiff = Tiff(filename, 'a');

% Loop through slices
for s = 1:dims(4)
    % Set tag structure for each frame
    tagstruct.ImageLength = dims(1);
    tagstruct.ImageWidth = dims(2);
    tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
    tagstruct.ExtraSamples = Tiff.ExtraSamples.AssociatedAlpha;
    tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
    tagstruct.SamplesPerPixel = 2;
    tagstruct.BitsPerSample = bitsPerSample;
    tagstruct.SampleFormat = sampleFormat;
    
    % Set the tag for the current frame
    outtiff.setTag(tagstruct);
    
    % Write the frame
    outtiff.write(array(:,:,:,s));
    
    % Create a new directory for the next frame
    if s ~= dims(4)
        outtiff.writeDirectory();
    end
end

% Close the file
outtiff.close();
end

Note that you're always opening the file in 'append' mode, so if you write to an existing file, you'll always add more frames to it.

[DGM]

See also:

https://www.mathworks.com/matlabcentral/answers/2079641-using-tiff-function-to-save-tiff-files#answer_1404741

This example uses a slightly more generalized variant of the TIFF helper function shown above.

Answer 2

[Image Analyst]

What is z and t?

If you want the loop to only go from c=1 to c=2, instead of this:

for c = 1:dims(3)

have this:

    for c = 1 : 2

Then I think it will write only the red channel and the blue channel.