[ImageJ-bugs] [Bug 1223] New: Unable to open .czi or BigTiff files
bugzilla at fiji.sc
bugzilla at fiji.sc
Wed Feb 10 18:55:07 CST 2016
http://fiji.sc/bugzilla/show_bug.cgi?id=1223
Bug ID: 1223
Summary: Unable to open .czi or BigTiff files
Product: Fiji
Version: unspecified
Hardware: Macintosh
OS: Mac OS
Status: NEW
Severity: normal
Priority: P4
Component: Plugins
Assignee: imagej-bugs at imagej.net
Reporter: jorgens at ohsu.edu
CC: jorgens at ohsu.edu
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
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