[ome-users] LSM import failed.

[Jerome Avondo]

Hi Colin,

Just (re)-tested the problematic LSM files with the updated 4.2.1 importer & server that are available to download from the main OMERO site,

This file is one of many that fail:

http://cmpdartsvr1.cmp.uea.ac.uk/downloads/data/All_tub_40_25min_01__Sum.lsm

And I still get the exact same error, and in the importer error log: "java.io.EOFException: Attempting to read beyond end of file"

Exact version numbers from OMERO.importer

Version: Beta4.2.1-r8614-Beta4.2-b41
Bioformats: 4.2.1-DEV (SVN 7178, 9 November 2010)

What version did you use to get it to work?
Thanks,

Jerome.

> Date: Thu, 11 Nov 2010 13:32:12 +0000
> From: c.blackburn at dundee.ac.uk
> To: jeromeavondo at msn.com
> CC: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] LSM import failed.
> 
> Hi Jerome,
> 
> On 11/11/2010 12:44, Jerome Avondo wrote:
> > Hi guys,
> >
> > I have found a couple of LSM files that seem to be failing to load/import...
> >
> > I initially tried with OMERO.importer (4.2) and it generates the error
> > attached as a screenshot, (errorpng.png)
> > And I also tried to test importing it with Fiji, using the trunk of
> > bioformats, and it also crashes, see the attached log file for the error
> > (log.txt)
> >
> > So I believe this is a bug.
> >
> > The dataset has been made available and you can download it from here:
> > http://cmpdartsvr1.cmp.uea.ac.uk/downloads/data/All_tub_40_25min_01__Sum.lsm
> 
> I've just tested this file with the imminent 4.2.1 release and it 
> imports okay.
> 
> > I also have some other LSM files that are failing with the
> > OMERO.importer (4.2) but which open fine in FIJI using the trunk of
> > bioformats.
> > So I guess those bugs are resolved, and I just have to wait for a newer
> > version of the importer.
> 
> Hopefully that wait won't be too much longer!
> 
> > Which leads me to my second question:
> > How safe is it for me to just update the bioformats library manually in
> > the OMERO tools, such that the second scenario can be easily resolved?
> >
> > And ideally it would be great that the OMERO tools always check and use
> > the trunk of bioformats, such that we always have the best
> > capabilities/latest bug fixes without having to wait for OMERO releases,
> > kinda like what FIJI does ie: always pull the trunk, but I guess there
> > are probably some other aspects/issues I am neglecting for why you guys
> > don't do this..
> > Just a wish list/feature really :)
> 
> The automatic updating of Bio-formats is on our to-do list
> 
> Cheers,
> 
> Colin
 		 	   		  
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