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Ome-metadata distributed across multiple tiff-files

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Ome-metadata distributed across multiple tiff-files

Postby stran » Mon Oct 27, 2014 12:59 pm

I am currently trying to implement use of the ome-xml metadata when writing my data to tiff-files.
For a timelapse I would save one time-point with a z-stack in one file.
As I understand the ome-xml wants the name of files and their UUIDs of all future timepoints already in this first file. In my eyes this requires reopening all images after the acquision and replacing/updating the meta data.
Is this correct or could I as an alternative only assemble the metadata for all past timepoints such that only the last file will contain the complete information?
Or in this respect, would it be better just to have one seperate ome-xml-file and save no further information within the tiffs?

Posts: 1
Joined: Fri Oct 24, 2014 8:32 am

Re: Ome-metadata distributed across multiple tiff-files

Postby ajpatterson » Tue Oct 28, 2014 10:46 pm

Hello Dan,

Yes, if you are writing the data as you collect it then you would need to re-open each tiff file to inject the correct xml at the end if you are storing the data in this manner.

There are three possible file arrangements:

* Single file: One single (possibly very large) file 'mydata.ome.tiff' that contains all the pixel data and metadata.
* Multi file: A collection of two or more ome.tiff files. Each file contain all the metadata but only a part of the pixel data. This file structure means that even a partial collection of the files are guaranteed to contain all the metadata.
* Tiffs with companion file: A collection of .ome.tiff files that each contain part of the pixel data but none of the metadata. Their ome-xml block is simply a pointer to the metadata companion stored as an .ome.xml file. This has both advantages and disadvantages, if the ome.xml file is lost, all the metadata is lost. If used for for freshly collected data it is a structure that can be faster to write, but if the collection process is interrupted all metadata can be lost.

Hope this helps,

Andrew Patterson
Software Developer, Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression
University of Dundee
Posts: 50
Joined: Fri May 01, 2009 11:18 am

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