Writing multidimensional TIFF files using imwrite

Hi, I'm trying to write multidimensional TIFF files (also known as "hyperstacks" in ImageJ). For example, the "dimensions" will be microscopy attributes, such as fluorescence channel, timepoint, stage position, etc. I have an example below. I tried using the imwrite "append" mode in a nested for loop but it simply created a 21x1 stack, not a 7x3 as I had hoped. Any suggestions? Thanks.

% A is 7x3 cell array containing all images
outputFileName = 'img_stack.tif'
  for j = 1:3 %channel number
      for i = 1:7 % timepoint
          imwrite(A{i,j}, outputFileName,'writemode','append','Compression','none');
      end
  end

[Curtis Rueden]

See also this question on StackOverflow. I recommend using the Bio-Formats library to export as OME-TIFF.

Answer 1

[Kouichi C. Nakamura]

I recommend to use ijmshow in conjunction with Fiji's ImageJ-MATLAB.

https://github.com/kouichi-c-nakamura/ijmshow

addpath '/Applications/Fiji.app/scripts' % depends your Fiji installation
ImageJ

imp = ijmshow(I,'YXCZT') 
% I is 5D array of uint8 or uint16
% the second argument determines which dimension represents what
% imp is a 5D hyperstack

ij.IJ.saveAsTiff(imp, 'image1.tif');

Answer 2

[Walter Roberson]

The information I find suggests that ImageJ parses the Tiff ImageDescription tag to determine the arrangement. I would need to study an example to determine the proper order.

imwrite() cannot write the ImageDescription tag; you would need to use the Tiff class for that.