Matlab only opens first frame of multi-page tiff stack

I've created multi-page tiff files with a macro in ImageJ, and I'm now trying to open it using matlab, but I can only access the first frame.

Here is the result of imfinfo(filename). Accordingly, I get

length(imfinfo(filename)) = 1

Filename: [1x129 char]
              FileModDate: '28-nov-2013 12:27:51'
                 FileSize: 6.7905e+09
                   Format: 'tif'
            FormatVersion: []
                    Width: 512
                   Height: 512
                 BitDepth: 8
                ColorType: 'grayscale'
          FormatSignature: [77 77 0 42]
                ByteOrder: 'big-endian'
           NewSubFileType: 0
            BitsPerSample: 8
              Compression: 'Uncompressed'
PhotometricInterpretation: 'BlackIsZero'
             StripOffsets: 932625
          SamplesPerPixel: 1
             RowsPerStrip: 512
          StripByteCounts: 262144
              XResolution: []
              YResolution: []
           ResolutionUnit: 'None'
                 Colormap: []
      PlanarConfiguration: 'Chunky'
                TileWidth: []
               TileLength: []
              TileOffsets: []
           TileByteCounts: []
              Orientation: 1
                FillOrder: 1
         GrayResponseUnit: 0.0100
           MaxSampleValue: 255
           MinSampleValue: 0
             Thresholding: 1
                   Offset: 8
         ImageDescription: 'ImageJ=1.47q
 images=25900
 slices=25900
 loop=false

However if I open the same tif file in ImageJ, then I can read and scroll through the 25900 frames...The weird thing is that matlab can read previous multipage tiff I had created in imageJ without my batch macro...

I don't understand what's happening...any help would be greatly appreciated ! Thanks, Steven

[Walter Roberson]

How are you attempting to do the reading?

Answer 1

[Christoph]

ImageJ only writes the first IFD for TIFF files larger than 4GB at the beginning of the file.

The other IFD entries are placed at the end of the TIFF file.

ImageJ is able to read such files because it sees "images=n" in the ImageDescription tag and realizes it needs to open n images.

As a workaround in MATLAB, you can try whether below code works. Note: This code assumes that the TIFF image has Stripped Planar Configuration and contains one strip per image. This might not work for all images but it could provide you a general idea about how to read such files generated by ImageJ using low-level I/O functions.

fileName = 'Mylarge.tif'; % Determine the number of image frames and the offset to the first image 
info = imfinfo(fileName)

This may yield something similar to (amongst others)

                     FileSize: 1.055313188500000e+10
                       Format: 'tif'
                FormatVersion: []
                        Width: 692
                       Height: 520
                     BitDepth: 16
                    ColorType: 'grayscale'
              FormatSignature: [77 77 0 42]
                    ByteOrder: 'big-endian'
               NewSubFileType: 0
                BitsPerSample: 16
                  Compression: 'Uncompressed'
    PhotometricInterpretation: 'BlackIsZero'
                 StripOffsets: 3342765
              SamplesPerPixel: 1
                 RowsPerStrip: 520
              StripByteCounts: 719680

Now determine the number of frames:

numFramesStr = regexp(info.ImageDescription, 'images=(\d*)', 'tokens');
numFrames = str2double(numFramesStr{1}{1});
% Use low-level File I/O to read the file
fp = fopen(fileName , 'rb');
% The StripOffsets field provides the offset to the first strip. Based on
% the INFO for this file, each image consists of 1 strip.
fseek(fp, info.StripOffsets, 'bof');
% Assume that the image is 16-bit per pixel and is stored in big-endian format.
% Also assume that the images are stored one after the other.
% For instance, read the first 100 frames
framenum=100;
imData=cell(1,framenum);
for cnt = 1:framenum
    imData{cnt} = fread(fp, [info.Width info.Height], 'uint16', 0, 'ieee-be')';
end
fclose(fp);

[Ashish Uthama]

Potential explanation for "The weird thing is that matlab can read previous multipage tiff I had created in imageJ without my batch macro...": I believe ImageJ switches to this (non-standard) tiff format when image size goes beyond 4GB, so if your previous images were smaller they would have been standard TIFF files that MATLAB could recognize.

Answer 2

[Ashish Uthama]

MATLAB R2020b has tiffreadVolume which supports non-BigTIFF volumes, greater than 4GB, created by ImageJ.