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<br>Hi Colin,<br><br>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,<br><br>This file is one of many that fail:<br><br>http://cmpdartsvr1.cmp.uea.ac.uk/downloads/data/All_tub_40_25min_01__Sum.lsm<br><br>And I still get the exact same error, and in the importer error log: "java.io.EOFException: Attempting to read beyond end of file"<br><br>Exact version numbers from OMERO.importer<br><br>Version: Beta4.2.1-r8614-Beta4.2-b41<br>Bioformats: 4.2.1-DEV (SVN 7178, 9 November 2010)<br><br>What version did you use to get it to work?<br>Thanks,<br><br>Jerome.<br><br>> Date: Thu, 11 Nov 2010 13:32:12 +0000<br>> From: c.blackburn@dundee.ac.uk<br>> To: jeromeavondo@msn.com<br>> CC: ome-users@lists.openmicroscopy.org.uk<br>> Subject: Re: [ome-users] LSM import failed.<br>> <br>> Hi Jerome,<br>> <br>> On 11/11/2010 12:44, Jerome Avondo wrote:<br>> > Hi guys,<br>> ><br>> > I have found a couple of LSM files that seem to be failing to load/import...<br>> ><br>> > I initially tried with OMERO.importer (4.2) and it generates the error<br>> > attached as a screenshot, (errorpng.png)<br>> > And I also tried to test importing it with Fiji, using the trunk of<br>> > bioformats, and it also crashes, see the attached log file for the error<br>> > (log.txt)<br>> ><br>> > So I believe this is a bug.<br>> ><br>> > The dataset has been made available and you can download it from here:<br>> > http://cmpdartsvr1.cmp.uea.ac.uk/downloads/data/All_tub_40_25min_01__Sum.lsm<br>> <br>> I've just tested this file with the imminent 4.2.1 release and it <br>> imports okay.<br>> <br>> > I also have some other LSM files that are failing with the<br>> > OMERO.importer (4.2) but which open fine in FIJI using the trunk of<br>> > bioformats.<br>> > So I guess those bugs are resolved, and I just have to wait for a newer<br>> > version of the importer.<br>> <br>> Hopefully that wait won't be too much longer!<br>> <br>> > Which leads me to my second question:<br>> > How safe is it for me to just update the bioformats library manually in<br>> > the OMERO tools, such that the second scenario can be easily resolved?<br>> ><br>> > And ideally it would be great that the OMERO tools always check and use<br>> > the trunk of bioformats, such that we always have the best<br>> > capabilities/latest bug fixes without having to wait for OMERO releases,<br>> > kinda like what FIJI does ie: always pull the trunk, but I guess there<br>> > are probably some other aspects/issues I am neglecting for why you guys<br>> > don't do this..<br>> > Just a wish list/feature really :)<br>> <br>> The automatic updating of Bio-formats is on our to-do list<br>> <br>> Cheers,<br>> <br>> Colin<br> </body>
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