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Bug 885 - Fiji error importing image sequence
Fiji error importing image sequence
Status: CONFIRMED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-07 15:28 CDT by David Knecht
Modified: 2014-08-07 15:49 CDT
2 users (show)

See Also:
Description David Knecht 2014-08-07 15:28:55 CDT 
Fiji gives an error message when importing a micro-manager generated folder of images using File/Import/Image Sequence.  It only happens if ImageJ2 use SCIFIO is checked.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  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-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  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: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140802115300)
Fiji: http://fiji.sc/update/ (last check:20140730150634)
LOCI: http://dev.loci.wisc.edu/fiji/ (last check:20140401145514)
OpenSPIM: http://openspim.org/update/ (last check:20140630095101)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140806102638)
Stowers: http://research.stowers.org/imagejplugins/updates/ (last check:20140805114656)

Files not up-to-date:
  ed946ffd (MODIFIED) 20140707150311 Contents/Info.plist
  5aaef494 (MODIFIED) 20140807131355 jars/bio-formats/formats-api.jar
  28a6e894 (MODIFIED) 20140807131357 jars/bio-formats/formats-bsd.jar
  a6f52489 (MODIFIED) 20140805112433 jars/bio-formats/formats-common.jar
  5d3f4991 (MODIFIED) 20140807131359 jars/bio-formats/formats-gpl.jar
  763477d8 (MODIFIED) 20140805112435 jars/bio-formats/jai_imageio.jar
  fcadebc0 (MODIFIED) 20140805112435 jars/bio-formats/mdbtools-java.jar
  3b60db12 (MODIFIED) 20140805112435 jars/bio-formats/metakit.jar
  b6d5fe26 (MODIFIED) 20140805112435 jars/bio-formats/ome-poi.jar
  3d9d9b1a (MODIFIED) 20140805112436 jars/bio-formats/ome-xml.jar
  9ae3dd1b (OBSOLETE) 20140805112432 jars/slf4j-log4j12-1.7.2.jar
  4f857c40 (LOCAL_ONLY) 20140413145817 macros/FWHM_Line.ijm
  10be5746 (LOCAL_ONLY) 20140729151030 macros/float stack macros.txt
  ee910016 (LOCAL_ONLY) 20140418174330 plugins/Macros/FWHM_Line.ijm
  948cfd99 (LOCAL_ONLY) 20140205160023 plugins/NL_Means_1.0.jar
  d08414c1 (LOCAL_ONLY) 20140415104556 plugins/Neuron_Growth.jar
  91fcf2c4 (LOCAL_ONLY) 20140418134827 plugins/RGB_Measure.class
  d1c9ab2c (LOCAL_ONLY) 20140204163744 plugins/SaveAsMovie_mac64.jar
  572ab775 (LOCAL_ONLY) 20140729152027 plugins/Stack_Deflicker.class
  896ab4ae (MODIFIED) 20140807131400 plugins/bio-formats_plugins.jar
Comment 1 Curtis Rueden 2014-08-07 15:49:18 CDT 
I assume this is the same problem described on the mailing list?
https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;8aed3b1f.1408

If so, it is a bug in the SCIFIO Micro-Manager format plugin. I was able to replicate the  error with one of our Micro-Manager datasets that you sent us previously ("micromanager/david/trial 2 part 3 40x_0").