[ome-users] pyramidal file systems

[Glen MacDonald]

thanks for the update.  I’m looking forward to Bio-Formats 5
Glen MacDonald
	Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
	Cellular Morphology Core
Center on Human Development and Disability
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
glenmac at uw.edu







On Feb 24, 2014, at 4:39 PM, Melissa Linkert <melissa at glencoesoftware.com> wrote:

> Hi Glen,
> 
>>> 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.
>> 
>> 
> *snip*
>> 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.
> 
> .vsi datasets in general do contain pyramids, but Roger is correct that
> they are not currently read by Bio-Formats.  We are in the process of
> correcting that, and expect the 5.0.1 version of Bio-Formats/OMERO to
> fully support this (unfortunately, it is a bit too late to make it in
> for 5.0.0).
> 
> Regards,
> -Melissa
> 
> On Mon, Feb 24, 2014 at 11:12:06AM +0000, Roger Leigh wrote:
>> 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
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