[ome-devel] Pyramidal OME-tiff

[Roger Leigh]

On 20/10/16 07:41, Benjamin Schmid wrote:

> I am currently looking into how to create tiled pyramidal ome-tiffs. I
> found them mentioned on a couple of websites, but couldn't find specific
> information about them (somewhere I read pyramidal ome-tiffs are not
> standardized). So do they exist? And is there any way to create them,
> via a script, or through the bioformats API? The key aspect is that
> OMERO recognizes that multiple resolutions belong to the same image (as
> it does for e.g. Aperio .svs files). Any information is grately
> appreciated.

A simple implementation of pyramidal TIFF is here:

https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/PyramidTiffReader.java

This is pretty basic and so should be simple to create a TIFF which will
be compatible with the reader, and this will result in images which
import into OMERO with all the pyramid levels being accessible with the
clients.

The key points are:
- The software tag must contain "Faas"
   (I'm not sure of the history here; I don't know if this is a software
package or vendor; we can always add additional ones if we want to make
it generic e.g. "ome-pyramid")
- There is one image IFD per resolution level, starting at the largest
size and then reducing down; each IFD should use tiles of an appropriate
size.

However, note this isn't an OME-TIFF, just a plain TIFF with some
required structure.  The OME data model does not yet have support for
pyramids/subresolutions, meaning that OME-TIFF isn't yet capable of
natively supporting pyramids.  If you do have additional metadata, that
would need adding after import into OMERO.


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096