icaoberg/Making an OME.TIFF using Bioformats

Created Wed, 09 Mar 2016 13:46:38 -0500 Modified Wed, 09 Mar 2016 13:46:38 -0500

In the previous example we used a 2D multitiff to make an OME.tiff. In this example we are going to use the files generated by demo3D01.

In this script we are loading each file, one by one, and then we are concatenating them.

files = { 'nucleus.tif', 'cell.tif', 'lysosome.tif', 'endosome.tif', ...
    'mitochondrion.tif', 'nucleoli.tif' };
addpath( './bfmatlab' );
omeimg = [];
for c=1:1:numel(files)
    file = files{c};
    img = tif2img( file );
    for z=1:1:size(img,3)
        %remember the indices mean xyzct
        omeimg(:,:,z,c,1) = img(:,:,z);
bfsave( omeimg, 'demo3D01.ome.tif', 'Compression', 'LZW' );

You can probably optimize the snippet. We want to use the compression option to make a smaller file. Using compression you get

$ du -h demo3D01.ome.tif
 14M  demo3D01.ome.tif

Without compression

$ du -h demo3D01.ome.tif
423M  demo3D01.ome.tif

Like the previous example, then you can import the image to the server