Bug 1250 – Issue using Bioformats to read ZVI files

Bug 1250 - Issue using Bioformats to read ZVI files


Summary:	Issue using Bioformats to read ZVI files

Status:	NEEDSINFO

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2016-03-22 11:24 CDT by Kathleen Proudfoot
Modified:	2016-03-22 13:55 CDT
CC List:	2 users (show)

See Also:

Description Kathleen Proudfoot 2016-03-22 11:24:34 CDT

Hello, 

The problem I'm currently having is that, although I hadn't updated FIJI recently, and was using this exact same version of the program to open ZVI files a few weeks ago, suddenly, FIJI can't open my files.  When I drag and drop, the familliar Bioformats Options window pops up, everything is set the same way it was when it was working before.  Then, once I hit 'OK', a second window which I've never seen before pops up asking me to how I'd like to group the list of files; by dimension, by name, or by file type.  However, no matter which option I chose, the file doesn't open, I just get an error message, something about a 'null pointer'.  

This is different but may be related to the bug that others have reported, where FIJI opens the ZVI file, but the channel colors are wrong.  I was having the problem a few weeks ago, but seemed to be able to fix it by playing around with the color channels settings.  

I'd appreciate any help you could give me on this matter, thanks!

Kathleen

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.10.5
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-466.1-11M4716
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-466.1
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160217090804)
Fiji: http://update.fiji.sc/ (last check:20160218075537)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20160314202643)
GDSC: http://sites.imagej.net/GDSC/ (last check:20160314062358)
GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20160310054351)

Comment 1 Curtis Rueden 2016-03-22 13:55:00 CDT

Try unchecking the "Group files with similar names" option.

Also: did you place additional files into the same directory as the ZVI file? Bio-Formats takes the liberty of scanning the directory for other files named in a similar way. For example, if you had:

   /Users/jdoe/embryo1.zvi

And then later you added:

   /Users/jdoe/embryo2.zvi

Then Bio-Formats would notice the 1-2 pattern and want to import them together, at least when the "Group files with similar names" option is checked.