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Bug 1223 - Unable to open .czi or BigTiff files
Unable to open .czi or BigTiff files
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2016-02-10 18:55 CST by Danielle Jorgens
Modified: 2016-04-26 17:03 CDT
2 users (show)

See Also:
Description Danielle Jorgens 2016-02-10 18:55:07 CST 
Hello, 

After previously being able to open and interact with both .czi and the BigTiff files I suddenly cannot.  I've been using BioFormats to import the images and selecting what I think are the appropiate check boxes.  The images are 2D, taken on a Zeiss Axioscanner in .czi format with JPXR compression.  The BigTiffs were generated from these .czis within the Zen software.  All of the images are between 500MB and 8GB.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.5
  java.version => 1.8.0_73
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_73-b02
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.73-b02
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160121035533)
Fiji: http://update.fiji.sc/ (last check:20160126102757)

Files not up-to-date:
  96a5c0e2 (MODIFIED) 20160210093946 Contents/Info.plist
  80e5d193 (MODIFIED) 20160125154925 jars/ij-1.50e.jar
  76b56dbc (LOCAL_ONLY) 20151207181220 plugins/DiameterJ_1-016.ijm
  f48d1368 (LOCAL_ONLY) 20151207181251 plugins/DiameterJ_Segment.ijm
  ec17890b (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/JHotDraw.jar
  91ece67d (LOCAL_ONLY) 20140123090208 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/JWlz.jar
  36cb5c0a (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/TableLayout.jar
  c3a86bd0 (LOCAL_ONLY) 20140123090208 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/assumeng.jar
  7c4005e7 (LOCAL_ONLY) 20050801102630 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis-wsdl4j.jar
  364315a9 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis.jar
  3370a633 (LOCAL_ONLY) 20070427143948 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis2-saaj.jar
  0af1624e (LOCAL_ONLY) 20140714161754 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/backport-util-concurrent.jar
  07f50124 (LOCAL_ONLY) 20150427193612 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz-javadoc.jar
  ab21bcc1 (LOCAL_ONLY) 20150427193542 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz-sources.jar
  63fdcaa4 (LOCAL_ONLY) 20150427193618 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz.jar
  189f61fa (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/bufr.jar
  94e35e33 (LOCAL_ONLY) 20150427193306 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common-javadoc.jar
  3646964f (LOCAL_ONLY) 20150427193302 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common-sources.jar
  c0f30819 (LOCAL_ONLY) 20150427193306 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common.jar
  940245e0 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-codec.jar
  64d8a654 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-collections.jar
  86ab9004 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-digester.jar
  9e9eb622 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-discovery.jar
  d59d3e4c (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-io.jar
  f6139801 (LOCAL_ONLY) 20100225002342 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-lang.jar
  fa9b8239 (LOCAL_ONLY) 20141210140056 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-logging.jar
  60a83b54 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-validator.jar
  abf211c5 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ehcache-core.jar
  e33cecc2 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/grib.jar
  2cd0d04c (LOCAL_ONLY) 20141125101518 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/guava.jar
  85c28658 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/hibernate-jpa-2.0-api.jar
  0c6e277e (LOCAL_ONLY) 20141210140056 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpclient.jar
  9f61e37d (LOCAL_ONLY) 20141210140056 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpcore.jar
  d216e98a (LOCAL_ONLY) 20141210140056 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpmime.jar
  1911c9e1 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-glacier2.jar
  b1d709fb (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-grid.jar
  c49b8fa2 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-storm.jar
  53aa5393 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice.jar
  84b54b46 (LOCAL_ONLY) 20150218193626 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ij.jar
  6ce638fb (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ini4j.jar
  f1b65457 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/java-getopt.jar
  c827227f (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/java-image-scaling.jar
  e72f9b2b (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jaxrpc.jar
  07f15e96 (LOCAL_ONLY) 20140724163642 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jcommon.jar
  c4eeeb8f (LOCAL_ONLY) 20140731133446 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jfreechart.jar
  5defc8da (LOCAL_ONLY) 20150320205720 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jhdf5.jar
  df7a0b63 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jna.jar
  4c09d41c (LOCAL_ONLY) 20140123090208 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/joda-time.jar
  4a754817 (LOCAL_ONLY) 20140929140200 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/kryo.jar
  b47bd885 (LOCAL_ONLY) 20150427193148 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/lwf-stubs.jar
  ab8ff4ee (LOCAL_ONLY) 20150218193636 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/metadata-extractor.jar
  16b765c2 (LOCAL_ONLY) 20140929140200 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/minlog.jar
  c74b45b0 (LOCAL_ONLY) 20150427193258 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql-javadoc.jar
  0436d2f4 (LOCAL_ONLY) 20150427193246 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql-sources.jar
  6267f51d (LOCAL_ONLY) 20150427193258 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql.jar
  66de339f (LOCAL_ONLY) 20140905201058 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/native-lib-loader.jar
  a51a31db (LOCAL_ONLY) 20140123090208 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/netcdf.jar
  aff28c0e (LOCAL_ONLY) 20140929140200 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/objenesis.jar
  18382f06 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ome-java.jar
  7af6ddeb (LOCAL_ONLY) 20140123090208 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/perf4j.jar
  b3056152 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/platform.jar
  4ef2cfd3 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/poi.jar
  eedc0cd9 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/serializer.jar
  5085d943 (LOCAL_ONLY) 20140321135832 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/slf4j-api.jar
  228d9879 (LOCAL_ONLY) 20150427193144 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/specification.jar
  ba32bfdf (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/swingx.jar
  c8694e76 (LOCAL_ONLY) 20140123090126 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xalan.jar
  93f166fd (LOCAL_ONLY) 20150218193636 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xercesImpl.jar
  a5c15945 (LOCAL_ONLY) 20150218193636 plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xmpcore.jar
  d428b86d (LOCAL_ONLY) 20150427194034 plugins/OMERO.insight-ij-5.1.1-ice35-b43/omero_ij.jar
  3d1bc91a (LOCAL_ONLY) 20151208110612 plugins/OrientationJ.txt
  c8bd9352 (LOCAL_ONLY) 20151207181310 plugins/OrientationJ_.jar
  f5e32ac2 (LOCAL_ONLY) 20151207181301 plugins/Skeleton_Intersections.jar
Comment 1 Curtis Rueden 2016-04-26 17:03:50 CDT 
Sorry for the long delay in reply.

Can you please describe what goes wrong when you try to open them? Do you receive an error message? What does it say? Etc. http://imagej.net/Bug_reporting_best_practices

Depending on the error message, you may end up needing to report this bug to the OME team, responsible for the Bio-Formats plugin:

www.openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html