[ome-users] support for LSM z-stacks and lambda-stacks

[Curtis Rueden]

Hi Shalin,

Have LSM (Zeiss LSM 510 ones) been supported by OMERO? I have installed
> ver.3-beta2.3 and when I imported a lambda-stack, the importer didn't
> recongnize pixel sizes.
>

Yes, Zeiss LSM has been supported in OMERO since at least Beta 2.1. A
complete list of formats supported by OMERO can be found here:
http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats

OMERO relies on Bio-Formats to parse the files, so if the pixel sizes were
missing or wrong, it is probably a bug in Bio-Formats. You can find out by
open your file in ImageJ with the Bio-Formats Importer plugin (see <
http://www.loci.wisc.edu/ome/formats.html>, choosing Image > Properties from
the menu, and looking to see what the Pixel Width, Pixel Height and Voxel
Depth values are. If they are 0.0, blank or NaN, then they were not parsed.

If you find that there is a bug with Bio-Formats reading your LSM metadata,
and you can send me a sample dataset demonstrating the issue, we will
investigate the problem. I can send you FTP information offline if you need
a place to upload files. To be clear, fixing the bug in Bio-Formats will fix
the problem for a future release of OMERO, as well.

-Curtis

On Jan 28, 2008 9:47 AM, Shalin Mehta <shalin.mehta at gmail.com> wrote:

> Dear all,
>
>  Have LSM (Zeiss LSM 510 ones) been supported by OMERO? I have installed
> ver.3-beta2.3 and when I imported a lambda-stack, the importer didn't
> recongnize pixel sizes.
>
> Cheers
> Shalin
>
> --
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> Shalin Mehta
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> blog: shalin.wordpress.com
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>
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> National Cancer Centre, Singapore 169610
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