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Bug 78 - LOCI Bio-Formats constantly opens extra hyperstack of Leica LIF
LOCI Bio-Formats constantly opens extra hyperstack of Leica LIF
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P3 minor
Assigned To: Curtis Rueden
Depends on: 57
Blocks:
 
Reported: 2009-09-17 15:33 CDT by Andrew Vaughan
Modified: 2010-07-29 23:17 CDT
1 user (show)

See Also:

Description Andrew Vaughan 2009-09-17 15:33:13 CDT
When I attempt to open a Leica LIF confocal stack FIJI opens a hyperstack of the data in addition to whatever the specified 'View Stack With' option was. For example, if I tried to open a 2 channel XYZ stack with the Standard Image J settings then this would open (incidentally, with an unwanted colour LUT matching the setting for the first channel), and so would a hyperstack of the same data. If I specify Hyperstack in the Bio-Formats Importer then two hyperstacks open. I am using a version of FIJI updated today (17/9/09) on an Intel iMac running OS 10.4.11 with Java version 1.5.0_13 from Apple.

The data should not have a CLUT applied if this is not specified, and it should not open an extra hyperstack if this is not asked for in the Bio-Formats Importer.
Comment 1 Curtis Rueden 2010-01-08 20:15:52 CST
Vytas Bindokas also reported this issue several months ago, but it is not duplicable on every system. The problem is very likely due to the Importer plugin calling the Stack Colorizer and/or Stack Slicer plugins, both of which temporarily duplicate the image stack. The refactoring of the Importer plugin (Bug 57 here and ticket #310 in LOCI Trac) will likely also resolve this issue.
Comment 2 Curtis Rueden 2010-07-29 23:17:08 CDT
This issue is fixed as of Bio-Formats 4.2. Please reopen if the problem reoccurs.