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Bug 96 - LOCI Bio-Formats Importer doesn't handle Leica LIF XZY stacks well
LOCI Bio-Formats Importer doesn't handle Leica LIF XZY stacks well
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P3 major
Assigned To: Curtis Rueden
Depends on:
Blocks:
 
Reported: 2009-10-23 10:33 CDT by Andrew Vaughan
Modified: 2010-02-01 21:05 CST
1 user (show)

See Also:
Description Andrew Vaughan 2009-10-23 10:33:00 CDT 
The current (as of 23/10/09) version of Bio-Formats in FIJI doesn't sort the X, Y, Z and channels dimensions correctly for XZY stacks in Leica LIF files. These are where the fast scanning galvo stage insert is used to generate stacks in a plane orthogonal to the usual XYZ. Note that stable version 4 of Bio-Formats from June this year handles them correctly in Image J as I asked Melissa Linkert to fix this for me.
Comment 1 Curtis Rueden 2010-01-08 20:08:19 CST 
The latest version of Bio-Formats in Fiji is now dated September 9th (newer than the June release of 4.0.0). So, can someone confirm whether the XZY functionality for LIFs is working in Fiji now?
Comment 2 Curtis Rueden 2010-01-20 19:12:20 CST 
Since no one commented, I'm closing this bug. Please reopen if there is a continuing problem.
Comment 3 Andrew Vaughan 2010-01-20 19:27:42 CST 
Sorry for the silence. I've been busy. The Importer still doesn't open XZY stacks correctly. Melissa put a trunk build on the LOCI website on 7/4/09 that worked correctly in Image J and still does. I recently installed a trunk build from 25/11/09 and the XZY support is broken again. I went back to the 7/4/09 version and that fixed it. Something changed between those to versions. It's never been right in FIJI. I'll be happy to submit an example data set if necessary.
Comment 4 Curtis Rueden 2010-02-01 21:05:35 CST 
Hopefully, r5871 in the Bio-Formats SVN repository corrects this issue. For more details, see:
https://skyking.microscopy.wisc.edu/trac/java/changeset/5871