2016.11.14 22:02 "Re: [Tiff] Right way to make a multi-resolution pyramid", by Roger Leigh

On 14/11/2016 21:16, Paavo Helde wrote:

On 14.11.2016 20:16, Kemp Watson wrote:

> Hi all:

What is the “correct” or canonical way to make a (tiled) multi-resolution pyramid in TIFF?

>> Most implementations I’ve seen simply chain top-level IFDs together,

starting with the base or full-res layer, and going smaller from there to

the apex. this seems wrong to me.

You are right, sub-IFDs would be more appropriate. However, sub-IFDs are not so well supported by various TIFF readers. That was the reason why in my company when they were working out the pyramidal TIFF schema a couple of years ago they still went with top-level IFD-s.

That's the way one of the Bio-Formats readers handles it as well:

https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/PyramidTiffReader.java (loop at line 129 just iterates over the IFDs to find the subresolutions)

The software vendor is "Faas", which is from http://jcb.rupress.org/content/198/3/457

http://jcb.rupress.org/content/198/3/271 (wow, can't believe that was four years ago now). This is a 921600 x 380928 pixel image using this format, all from a single tiled BigTIFF with pyramid levels.

Online viewer here: http://v.jcb-dataviewer.glencoesoftware.com/webclient/img_detail/201/ - it's quite fun to look around and the number of pyramid levels is ridiculous (12 power of two reductions).

That's a sort-of standard format in that it's supported by a lot of biological image analysis and visualisation tools using Bio-Formats for file I/O.

[Incidentally, my work on libtiff stuff like CMake is for its sister project OME Files C++ which is a conversion of the core Bio-Formats APIs and functionality for C++, and libtiff is a core part of that functionality.]

This use of multiple IFDs doesn't work with multi-dimensional images though, for that I can see SUBIFDs would work much better. This is one thing I've been unsure of how to make use of with the libtiff API though. How to you create the subifd to be able to add it to the tag, without it being in the main list of IFDs? And can you write them out from largest to smallest? Or do you need to write the smaller images first so you can reference them in the larger ones?

Doing this is on my TODO list, and so it's quite nice this came up on the list in the meantime.

Regards,
Roger