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Bug 948 - Two pictures only open totally distorted with Fiji - but work in standard image-J
Two pictures only open totally distorted with Fiji - but work in standard ima...
Status: CONFIRMED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-10-28 15:11 CDT by dergicy
Modified: 2014-10-29 09:32 CDT
2 users (show)

See Also:

Attachments
JPG File, loading plain wrong in FIJI 1.49j10 but loading correct in image-j 1.49i and 1.49j (98.25 KB, image/jpeg)
2014-10-28 15:15 CDT, dergicy

Description dergicy 2014-10-28 15:11:58 CDT 
Just open the provided jpeg to reproduce the error.

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: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: E:\0000_M~1\00_FIJI\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => E:\0000_M~1\00_FIJI\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141026020028)
Fiji: http://fiji.sc/update/ (last check:20141023165357)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20140827184014)
Comment 1 dergicy 2014-10-28 15:15:50 CDT 
Created attachment 219
JPG File, loading plain wrong in FIJI 1.49j10 but loading correct in image-j 1.49i and 1.49j
Comment 2 Johannes Schindelin 2014-10-29 04:13:33 CDT 
I can reproduce, or at least I think that I reproduced the issue. It happens when SCIFIO is enabled in Edit>Options>ImageJ2... and it does not *distort* the image, but it *saturates* it. It almost looks as if the display range was set to 0-28 and then the "Apply" button was hit in the Brightness&Contrast dialog.

Since this does not happen to *all* JPGs, would you have an idea what makes your JPG special?
Comment 3 dergicy 2014-10-29 09:32:27 CDT 
I wish I knew, I made 3 pictures with the microscope. (and many more, that work...)

1 Brightfield
1 with green fluoresence (by exciting with blue light)
1 with red fluoresence (by exciting with green light)

Both fluoresence pictures produce the "saturation"-error, the BF does not.

BUT I made more pictures from the same cell sample, at other positions of the counting chamber. I did not check all, but the error has yet to occur again.

I did not change any setting at all on the microscope side, either.

I tried opening the picture with FIJI in original and after resizing in Irfanview, but the "saturation"-bug still happens.