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Writing multidimensional TIFF files using imwrite

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Jonathan Cheng
Jonathan Cheng on 3 May 2016
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

Answers (2)

Kouichi C. Nakamura
Kouichi C. Nakamura on 3 May 2018
I recommend to use ijmshow in conjunction with Fiji's ImageJ-MATLAB.
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');

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Walter Roberson
Walter Roberson on 3 May 2016
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.

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