[ome-users] Sporadic errors on *.lsm images - any prior reports?

Taylor, Ronald C ronald.taylor at pnl.gov
Mon Sep 20 05:02:18 BST 2010


Thanks for giving the file a try. Question: I included two LSM files in my initial email - one that works upon import, one that fails (shows up as black box) after an import error. The file that you tried and that failed for you was the one that I labeled as the failure, right? Just want to make sure that you are replicating our failure. The other file (the one labeled OK) works for you?

Ronald Taylor, Ph.D.
Computational Biology & Bioinformatics Group
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, Mail Stop J4-33
Richland, WA  99352 USA
Office:  509-372-6568
Email: ronald.taylor at pnl.gov

-----Original Message-----
From: Woodbridge, Mark R [mailto:m.woodbridge at imperial.ac.uk] 
Sent: Sunday, September 19, 2010 3:29 AM
To: Taylor, Ronald C; ome-users at lists.openmicroscopy.org.uk
Subject: RE: Sporadic errors on *.lsm images - any prior reports?

Hi Ron,

I get an ArrayIndexOutOfBoundsException when importing your file into OMERO 4.2 so perhaps one for the devlopers to investigate. We haven't had problems with any other lsm files.

From: ome-users-bounces at lists.openmicroscopy.org.uk [ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Taylor, Ronald C [ronald.taylor at pnl.gov]
Sent: 19 September 2010 06:45
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] Sporadic errors on *.lsm images -  any prior reports?

Hello folks,

We are using OMERO 4.2.0 on our Mac server. One of our scientists is importing Zeiss LSM files (see http://en.wikipedia.org/wiki/LSM_(Zeiss) ). He is seeing sporadic errors upon import. Some files show up fine, others come in as completely dark images.

All of the files come from the same microscope and the same software. So - this is a mystery to us. At present, this is the only importing error we are seeing in OMERO 4.2.0 - other file types are not having any problems so far.

I have attached two LSM files - one that displays OK upon import, the other which causes an error and shows up dark. Can someone take a look in their own 4.2.0 system and see if they can duplicate the error?

Also - is this a known bug? Have other people reported errors involving LSM files?

   Ron Taylor
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