[ome-users] OMERO.importer and LSM files

[Melissa Linkert]

Hi,

This was an issue with Bio-Formats' LSM reader.  It has been fixed, and a
new version of OMERO beta 2.2 that incorporates these changes will be
available within the next few days.   The next major version of Bio-Formats
will also include the fix for this problem.

With the new version of the importer, a 400MB LSM file should import in
under 15 minutes.

Regards,
-Melissa

On 11/5/07, McCaughey, Michael J <michael.j.mccaughey at vanderbilt.edu> wrote:
>
>  Hey all-
> I'm trying to use Omero.importer to import Zeiss .lsm files and running
> into some issues.
>
> My server is a dual Opteron box with 4GB ram, hardware RAID, gigabit NIC.
> Not much running on it other than FC6 and packages required by OMERO, no
> other users. Omero is the most recent pre-compiled binary. Client is a dual
> G5 with 2GB ram and gigbitNIC, importer is v2.1 beta. Client and server
> are connected through a dedicated gigabit switch with no other network
> traffic. Performance of server, client, and network should be pretty
> reasonable.
>
> The .lsm files are captured from both LSM510 and LSM 5Live confocals.
>
> The problem is, I'm finding .lsm files very slow to import. Like hours.
> For example, I have a 403MB .lsm file (256x256, 6 z slice, 390 time) that I
> can ftp from client to server in 19 seconds.  It took 5 hours and 2minutes
> to import it into Omero. Once imported, it seems to be fine.
>
> This seems only to affect lsm files, .tifs (much smaller ~4MB) go over in
> seconds.
>
> Any suggestions?
>
> Thanks,
> Mike
>
> Michael J. McCaughey, PhD
> Molecular Physiology and Biophysics
> U9203 MRBIII
> 6-6175
>
>
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>
>
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