[ome-users] Storing 6D and 7D in OME-XML & OME-TIFF

[Andrew Patterson]

Hello,

Following on from discussions we have had after the release of the 6D and 7D solution we have decided to make a small change. The addition of 8D.

We've received feedback suggesting a ModuloAlongC option— allowing the storage of up to 8D dimensions.  All the examples we currently know of use up to 7D; this change allows us to support an additional dimension, should it become necessary (undoubtedly it will). We reviewed the implication of this change and it looks like it can definitely be added.  This means that the Modulo option now enables up to 8D imaging.

The web page has been updated to include ModuloAlongC.

The web page has a new URL:
http://www.openmicroscopy.org/site/support/file-formats/6d-7d-and-8d-storage
but the old link will continue to work and redirect to the new page.

We welcome your suggestions for further improvements as always. Comments can be emailed to us or left on our forums: 
http://www.openmicroscopy.org/community/

Thanks again,

Andrew


On 16 Sep 2011, at 15:02, Andrew Patterson wrote:

> Hello,
> 
> We have been doing some further work on fitting data that requires more than 5 dimensions into the OME data model. Our plan in the long term is to move to using an N-dimensional model but this will take a large amount of work to the Bio-Formats, the OMERO server and clients. In the short term we have devised a solution we can put in place that will allow up to 7 dimensions in our existing model. We have called this the Modulo solution.
> 
> This solution relies on using the Z and T dimensions to each store an extra dimension. The description of the extra dimensions are stored in StructuredAnnotation so the data looks like 5-D data, and can thus be stored in the current OME-TIFF and OMERO server.
> 
> Full details and sample files are available at:
> 
> http://www.openmicroscopy.org/site/support/file-formats/6d-and-7d-storage
> 
> When the OME model moves to be N-dimensional we can upgrade data stored in this structure.
> 
> We hope this proposal will work for your data. 
> 
> We welcome your suggestions for further improvements as always. Comments can be emailed to us or left on our forums: 
> http://www.openmicroscopy.org/community/
> 
> Thanks,
> 
> Andrew
> 
> ----
> Andrew Patterson
> ajpatterson at lifesci.dundee.ac.uk
> Software Developer, Open Microscopy Environment
> Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee
> 
>