Bioformats Ome-Tiff example with Tiles and Pyramids

Dear @ome,

Do you have any chance a ‘simple’ example of writing an ome-tiff file containing pyramids and tiles (to avoid the issue of a number of bytes > 2^31). I checked the bioformats example but I could only find:

Fyi, I’m writing a wrapper for bioformats and bigdataviewer, and I wanted to write an exporter for ome-tiff. I have a small example which works so far for a single Source provided it is an unsigned byte image. I wanted to generalize it for other types and for big images.

Best,

Nicolas

ping @Christian_Tischer

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We don’t have a simple example that includes both, the ImageConverter is a good example though it is more complicated. The number of bytes > 2^31 issue was specific to the ImageConverter code which has since been updated as part of 6.2.1 (https://github.com/ome/bioformats/pull/3424).

Looking at your sample code the parts of ImageConverter that would be of interest would be the convertTilePlane method (https://github.com/ome/bioformats/blob/develop/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java#L787) and getTile which also handles downsampling of tiles (https://github.com/ome/bioformats/blob/develop/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java#L1026).

If you are still stuck I can try and put together some sample code for you tomorrow which handles both without a lot of the extras in ImageConverter.

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