[ome-devel] Some file format suggestions

[Roger Leigh]

On 04/06/18 16:51, Andrew Brooks wrote:
> First, thanks for a very interesting couple of days learning all about
> OME and all the other TLAs :)
>
> I have a couple of suggestions for the developers which come from the
> geospatial community, who are solving similar problems. Maybe you've
> already heard of them, but if not:
>
> One is Cloud Optimised GeoTIFFs, if you ignore the Geo then you might
> find something of interest here: http://www.cogeo.org/in-depth.html
>
> The other is GeoPackage which goes a step further, it is a single-file
> format which stores raster (tiles and pyramids) plus vector, and the
> reason I thought about OMERO is your use of ROIs.

Dear Andrew,

Many thanks for the suggestions, which are much appreciated.  I have
added this as some additional notes on the existing design proposal here:

   https://github.com/openmicroscopy/design/pull/95

and you can see the full document here:


https://github.com/rleigh-codelibre/design/blob/da24df08a599b89383ec0ba90f866f73408b0e73/OME005/index.md

Unfortunately, the GeoTIFF design has the same cons as the proposal (A)
outlined above, which makes it unsuitable for OME-TIFF.  However, the
underlying design rationale for the "cloud optimised" GeoTIFF will be
implemented by us.  The use of tiles and subresolutions in proposal (C)
will provide exactly the same benefits despite the internal layout being
a little different.

GeoPackage looks very interesting.  I have been thinking about the
possibility of representing the OME-XML metadata in an SQLite DB, and
reusing an existing format is certainly something we could consider.
It's not something we will be able to do right now, but we will
certainly bear it in mind for the future.


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