Bug 1139 – Reading CZI series image returns empty image while all the metadata are ok

Bug 1139 - Reading CZI series image returns empty image while all the metadata are ok


Summary:	Reading CZI series image returns empty image while all the metadata are ok

Status:	RESOLVED MOVED

Product:	Fiji
Classification:	Unclassified
Component:	Bio-Formats
Version:	unspecified
Hardware:	PC Windows

Importance:	P5 critical
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2015-08-11 10:46 CDT by Sebastian Rhode
Modified:	2015-08-17 08:10 CDT
CC List:	2 users (show)

See Also:

Attachments
Empty thumbnails inside import dialog. (92.55 KB, image/png) 2015-08-11 10:46 CDT, Sebastian Rhode
Result Fiji - Empty image (233.26 KB, image/png) 2015-08-11 10:48 CDT, Sebastian Rhode
Test Dataset in ZEN - OK (743.72 KB, image/png) 2015-08-11 10:50 CDT, Sebastian Rhode

Description Sebastian Rhode 2015-08-11 10:46:34 CDT

Created attachment 255
Empty thumbnails inside import dialog.

Hi,

I downloaded today's version of Fiji and tried to open a CZI series file via BioFormats 5.1.3 (contains 8 series) as I did many time before. But when the window opens, where one can select which series to open, all the thumbnails are black (see screenshot).

The XML metadata see to be OK, but the resulting import image contains only zeros. This used to work before without any problems and as far as I remember it wasa even no problem with BF 5.1.3 some days ago...

The CZI image can be found here:

https://dl.dropboxusercontent.com/u/623476/Tiles1_CH%3D2_Z%3D3_T%3D2_B2_B4_SingleCZI.czi











Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: c:\Users\Public\DOCUME~1\FIJI_2~1/java/win64/jdk1.6.0_24//jre
  imagej.dir => c:\Users\Public\DOCUME~1\FIJI_2~1

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150722045527)
Fiji: http://fiji.sc/update/ (last check:20150724215809)

Comment 1 Sebastian Rhode 2015-08-11 10:48:11 CDT

Created attachment 256
Result Fiji - Empty image

Comment 2 Sebastian Rhode 2015-08-11 10:50:07 CDT

Created attachment 257
Test Dataset in ZEN - OK

Comment 3 Curtis Rueden 2015-08-17 08:10:34 CDT

Thanks, Sebastian.

As you probably know, Bio-Formats has its own issue tracking process, described here:
https://www.openmicroscopy.org/site/support/bio-formats5.1/about/bug-reporting.html

In future, reporting Bio-Formats issues with the OME team directly is the best course of action.

I know you already notified the OME team of this particular issue. In the interest of proper cross-linking, that thread is at:
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-August/005578.html