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Bug 592 - problem opening zvi files saved from Lighthsheet.Z1
problem opening zvi files saved from Lighthsheet.Z1
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
All All
: P5 blocker
Assigned To: Melissa Linkert
Depends on:
Blocks:
 
Reported: 2013-04-20 07:43 CDT by tomancak
Modified: 2015-04-21 11:19 CDT
3 users (show)

See Also:

Description tomancak 2013-04-20 07:43:32 CDT
Dear Melissa,

I know that the multi-view .czi files are not working yet. However we had a functional workaround that seemed to have stopped working now. 

We save every angle separately as a single .czi file. It used to be possible to open these in Fiji. 


Now what happens is that if I have 6 angle time lapse (715 timepoints) I can open the first 5 angles,

log From SPIM registration plugin
Opening '/projects/tomancak_lightsheet/Valia/Valia/spim_TL1_Angle1.czi' [1920x1060x130 type=uint16 image=Image<FloatType>]
spim_TL1_Angle1.czi sigma: 1.8 minPeakValue: 0.019
Found peaks (possible beads): 499

the sixth angle and all the subsequent ones give the following

(Sat Apr 20 14:25:21 CEST 2013): Starting Scale Space Bead Extraction for spim_TL1_Angle6.czi
LOCI.openLOCI(): More than one timepoint. Not implemented yet. Returning first timepoint
Opening '/projects/tomancak_lightsheet/Valia/Valia/spim_TL1_Angle6.czi' [1920x1060x130 type=uint16 image=Image<FloatType>]
Cannot normalize image spim_TL1_Angle6.czi, min=0.0  + max=0.0

I tried several later timepoints and they all come up empty - min and max = 0. My interpretation from reading the metadata is that the file thinks its a part of a long time series and returns the first time point which is not really there. 

I have literally terabytes of data saved that way and will not be able to process them unless this is fixed. 

I am happy to report more and send a few stacks (they are big).

Thanks for your help

PAvel

The full SPIM registration log is attached

[tomancak@n10 registration]$ xvfb-run -a /sw/users/tomancak/packages/Fiji.app/ImageJ-linux64 -Ddir=/projects/tomancak_lightsheet/Valia/Valia/ -Dtimepoint=1 -Dangles=1-6 -- --no-splash /projects/tomancak_lightsheet/Valia/Valia//jobs/registration/registration.bsh
12 cores available for multi-threading
init Bead_Registration dialog: tfSpimDataDirectory.getText() = 
Version 0.55
(Sat Apr 20 14:23:12 CEST 2013): Starting Bead Extraction
(Sat Apr 20 14:23:12 CEST 2013): Starting Scale Space Bead Extraction for spim_TL1_Angle1.czi
log4j:WARN No appenders could be found for logger (loci.formats.ClassList).
log4j:WARN Please initialize the log4j system properly.
Opening '/projects/tomancak_lightsheet/Valia/Valia/spim_TL1_Angle1.czi' [1920x1060x130 type=uint16 image=Image<FloatType>]
spim_TL1_Angle1.czi sigma: 1.8 minPeakValue: 0.019
Found peaks (possible beads): 499
(Sat Apr 20 14:23:40 CEST 2013): Starting Scale Space Bead Extraction for spim_TL1_Angle2.czi
Opening '/projects/tomancak_lightsheet/Valia/Valia/spim_TL1_Angle2.czi' [1920x1060x130 type=uint16 image=Image<FloatType>]
spim_TL1_Angle2.czi sigma: 1.8 minPeakValue: 0.019
Found peaks (possible beads): 432
(Sat Apr 20 14:24:12 CEST 2013): Starting Scale Space Bead Extraction for spim_TL1_Angle3.czi
Opening '/projects/tomancak_lightsheet/Valia/Valia/spim_TL1_Angle3.czi' [1920x1060x130 type=uint16 image=Image<FloatType>]
spim_TL1_Angle3.czi sigma: 1.8 minPeakValue: 0.019
Found peaks (possible beads): 405
(Sat Apr 20 14:24:33 CEST 2013): Starting Scale Space Bead Extraction for spim_TL1_Angle4.czi
Opening '/projects/tomancak_lightsheet/Valia/Valia/spim_TL1_Angle4.czi' [1920x1060x130 type=uint16 image=Image<FloatType>]
spim_TL1_Angle4.czi sigma: 1.8 minPeakValue: 0.019
Found peaks (possible beads): 442
(Sat Apr 20 14:24:57 CEST 2013): Starting Scale Space Bead Extraction for spim_TL1_Angle5.czi
Opening '/projects/tomancak_lightsheet/Valia/Valia/spim_TL1_Angle5.czi' [1920x1060x130 type=uint16 image=Image<FloatType>]
spim_TL1_Angle5.czi sigma: 1.8 minPeakValue: 0.019
Found peaks (possible beads): 492
(Sat Apr 20 14:25:21 CEST 2013): Starting Scale Space Bead Extraction for spim_TL1_Angle6.czi
LOCI.openLOCI(): More than one timepoint. Not implemented yet. Returning first timepoint
Opening '/projects/tomancak_lightsheet/Valia/Valia/spim_TL1_Angle6.czi' [1920x1060x130 type=uint16 image=Image<FloatType>]
Cannot normalize image spim_TL1_Angle6.czi, min=0.0  + max=0.0
spim_TL1_Angle6.czi sigma: 1.8 minPeakValue: 0.019
(Sat Apr 20 14:25:46 CEST 2013): Warning! Failed to compute subpixel localization SubpixelLocalization: [List<DifferenceOfGaussianPeak<T>> peaks] is empty.
Found peaks (possible beads): 0
(Sat Apr 20 14:25:46 CEST 2013): Finished Bead Extraction
(Sat Apr 20 14:25:46 CEST 2013): Starting Registration
Exception in thread "Thread-660" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at fiji.util.KDTree.<init>(KDTree.java:42)
	at fiji.util.KDTree.<init>(KDTree.java:37)
	at mpicbg.spim.registration.detection.descriptor.CoordSystem3d.extractCorrespondenceCandidates(CoordSystem3d.java:31)
	at mpicbg.spim.registration.bead.BeadRegistration$2.run(BeadRegistration.java:351)
	at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-657" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at fiji.util.KDTree.<init>(KDTree.java:42)
	at fiji.util.KDTree.<init>(KDTree.java:37)
	at mpicbg.spim.registration.detection.descriptor.CoordSystem3d.extractCorrespondenceCandidates(CoordSystem3d.java:31)
	at mpicbg.spim.registration.bead.BeadRegistration$2.run(BeadRegistration.java:351)
	at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-653" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at fiji.util.KDTree.<init>(KDTree.java:42)
	at fiji.util.KDTree.<init>(KDTree.java:37)
	at mpicbg.spim.registration.detection.descriptor.CoordSystem3d.extractCorrespondenceCandidates(CoordSystem3d.java:31)
	at mpicbg.spim.registration.bead.BeadRegistration$2.run(BeadRegistration.java:351)
	at java.lang.Thread.run(Thread.java:662)
spim_TL1_Angle2.czi<->spim_TL1_Angle3.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle1.czi<->spim_TL1_Angle3.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle1.czi<->spim_TL1_Angle5.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle1.czi<->spim_TL1_Angle2.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle3.czi<->spim_TL1_Angle5.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle2.czi<->spim_TL1_Angle5.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle2.czi<->spim_TL1_Angle4.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle3.czi<->spim_TL1_Angle4.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle1.czi<->spim_TL1_Angle4.czi: Not enough correspondences found 1, should be at least 12
Exception in thread "Thread-650" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at fiji.util.KDTree.<init>(KDTree.java:42)
	at fiji.util.KDTree.<init>(KDTree.java:37)
	at mpicbg.spim.registration.detection.descriptor.CoordSystem3d.extractCorrespondenceCandidates(CoordSystem3d.java:31)
	at mpicbg.spim.registration.bead.BeadRegistration$2.run(BeadRegistration.java:351)
	at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-651" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at fiji.util.KDTree.<init>(KDTree.java:42)
	at fiji.util.KDTree.<init>(KDTree.java:37)
	at mpicbg.spim.registration.detection.descriptor.CoordSystem3d.extractCorrespondenceCandidates(CoordSystem3d.java:31)
	at mpicbg.spim.registration.bead.BeadRegistration$2.run(BeadRegistration.java:351)
	at java.lang.Thread.run(Thread.java:662)
spim_TL1_Angle4.czi<->spim_TL1_Angle5.czi: Not enough correspondences found 0, should be at least 12
spim_TL1_Angle1.czi (id = 0) has 0 correspondences in 0 other views.
spim_TL1_Angle2.czi (id = 1) has 0 correspondences in 0 other views.
spim_TL1_Angle3.czi (id = 2) has 0 correspondences in 0 other views.
spim_TL1_Angle4.czi (id = 3) has 0 correspondences in 0 other views.
spim_TL1_Angle5.czi (id = 4) has 0 correspondences in 0 other views.
spim_TL1_Angle6.czi (id = 5) has 0 correspondences in 0 other views.
The total number of detections was: 2270
The total number of correspondence candidates was: 1
The total number of true correspondences is: 0
Successfully optimized configuration of 0 tiles after 202 iterations:
  average displacement: ?px
  minimal displacement: 179,769,313,486,231,570,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000.000px
  maximal displacement: 0.000px
Optimizer Matrices
ViewErrorStatistics.setViewSpecificError(): Warning! spim_TL1_Angle1.czi (id = 0) is not part of the structure of my view spim_TL1_Angle1.czi (id = 0)
spim_TL1_Angle1.czi (id = 0): is not connected to any other tile!
ViewErrorStatistics.setViewSpecificError(): Warning! spim_TL1_Angle2.czi (id = 1) is not part of the structure of my view spim_TL1_Angle2.czi (id = 1)
spim_TL1_Angle2.czi (id = 1): is not connected to any other tile!
ViewErrorStatistics.setViewSpecificError(): Warning! spim_TL1_Angle3.czi (id = 2) is not part of the structure of my view spim_TL1_Angle3.czi (id = 2)
spim_TL1_Angle3.czi (id = 2): is not connected to any other tile!
ViewErrorStatistics.setViewSpecificError(): Warning! spim_TL1_Angle4.czi (id = 3) is not part of the structure of my view spim_TL1_Angle4.czi (id = 3)
spim_TL1_Angle4.czi (id = 3): is not connected to any other tile!
ViewErrorStatistics.setViewSpecificError(): Warning! spim_TL1_Angle5.czi (id = 4) is not part of the structure of my view spim_TL1_Angle5.czi (id = 4)
spim_TL1_Angle5.czi (id = 4): is not connected to any other tile!
ViewErrorStatistics.setViewSpecificError(): Warning! spim_TL1_Angle6.czi (id = 5) is not part of the structure of my view spim_TL1_Angle6.czi (id = 5)
spim_TL1_Angle6.czi (id = 5): is not connected to any other tile!
(Sat Apr 20 14:25:47 CEST 2013): Finished Registration
Finished processing.
Comment 1 tomancak 2013-04-20 07:52:02 CDT
Update. 

The data reside in the very last timepoint of the series. I.e. metadata says that the t dimension is 333 which means if I import in bioformats the last tp (333) I get the data.

I hope this helps.

PAvel
Comment 2 Melissa Linkert 2013-04-20 07:57:42 CDT
"LOCI.openLOCI(): More than one timepoint. Not implemented yet. Returning first timepoint" is coming from imglib, not Bio-Formats:

http://trac.imagej.net/browser/ImgLib/imglib1/io/src/main/java/mpicbg/imglib/io/LOCI.java#L198

Do the problematic files open correctly if you open them with "Plugins > LOCI > Bio-Formats Importer"?  If not, then it would be useful to have one or two of them; if so, then this may not be a Bio-Formats issue.
Comment 3 tomancak 2013-04-20 08:01:43 CDT
No, the same problem occurs when opening from bioformats importer plugin. It thinks its loading a long time series, I have to click the time-point option and then specify the last timepoint.

PAvel
Comment 4 Melissa Linkert 2013-04-20 08:07:55 CDT
Then could you please upload one of the files, either through Fiji or as a zip file to http://qa.openmicroscopy.org.uk/qa/upload/?  I am about to get on a plane, but can take a look on Monday.
Comment 5 tomancak 2013-04-20 08:14:24 CDT
will do. I sent you a link in a private email.

One more piece of info the first 5 zvi files (5 of the 6 angles in first tp) have t dimnesion = 1. That's why they work.

Is there a way to reset the metadata to t = 1?

PAvel
Comment 6 Melissa Linkert 2013-04-23 09:19:58 CDT
As noted in a private email, I haven't been able to download the files due to permission errors.  If at least one of the non-working files can be made available today, then I can probably get a fix in this week's release of Bio-Formats; otherwise, the fix will have to wait until next week at earliest (and then won't be in a stable release for a while).
Comment 7 Johannes Schindelin 2013-07-07 10:18:20 CDT
PAvel: ping?
Comment 8 Curtis Rueden 2014-06-26 22:06:13 CDT
PAvel, how does the latest version of Bio-Formats handle this data? There have been lots of improvements to CZI by this point. Can this issue be closed? If not, please upload the offending file(s) as a ZIP through the OME QA system: http://qa.openmicroscopy.org.uk/qa/upload/
Comment 9 Curtis Rueden 2015-04-21 11:19:37 CDT
Presumed fixed. If there is still an issue, please report it to the Bio-Formats team:

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