[ome-users] pyramidal file systems

[Roger Leigh]

On 17/02/14 21:50, Glen MacDonald wrote:
> Hello,
> We are considering purchase of an Olympus VS120 slide scanner.    Does LOCI or OMERO fully support any of the pyramidal image formats for compression and scaling?  LOCI opens the .vsi files as full size images.

Dear Glen,

Several of the above formats are supported by Bio-Formats and OMERO.  An
overview of the formats we support is here:

http://www.openmicroscopy.org/site/support/bio-formats4/supported-formats.html

For the 4.4 releases of Bio-Formats and OMERO, we did not support native
access to the sub-resolution/pyramid data in big image file formats.
Each resolution level was presented as a separate image (series).  OMERO
computed pyramids on import for all of the big high-magnification
images, but this is quite slow.

In the 5.0 prereleases (and soon to be stable releases) of Bio-Formats
and OMERO, sub-resolutions may now be accessed directly via the
Bio-Formats API, and these are used directly by OMERO.  Formats which
make use of subresolutions and which are supported directly by
Bio-Formats include Aperio SVS, Hamamatsu NDPI, Imaris HDF and Leica
SCN.  Import and viewing of these formats is now very fast compared with
the 4.4 releases.

Olympus CellSens VSI images are supported, but we don't currently
support subresolutions for this format.  I'm not sure whether or not
this particular format does contain pyramids.  OMERO will certainly
generate pyramids for the images on import as it did for 4.4.

Note that for most of these formats, the original image file contains an
overview of the slide at a low magnification, plus one or more
higher-resolution images of specific areas (plus pyramids for some
formats).  While pyramids are supported transparently for formats which
provide them, the overview and individual high magnification images will
be shown as separate image series.  So the pixel data is all accessible,
but will be presented in a different way than some of the proprietary
viewers, which blend all the separate images into a single view.  We may
be able to support this mode of viewing in the future, but do not at
present.


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