[ImageJ-bugs] [Bug 1033] New: Issue with opening 14 bit images

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1033

            Bug ID: 1033
           Summary: Issue with opening 14 bit images
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: ann.wheeler at igmm.ed.ac.uk
                CC: ann.wheeler at igmm.ed.ac.uk

Pretty much all of the images we acquire are 14 bit. However Fiji is opening
them as 16 bit unsigned images and autoscaling. The issue is when we are
quantifying it is automatically rescaling the images. Seems like Fiji thinks it
is very helpful if it re- autoscales the image we just unscaled. 

The workaround is frustrating, in the Brightness and Contrast - Set display
range I would like to have an option in the Unsigned 16 bit option for 14 bit
images. There appear to be 8, 12, 15 and 16 bit options here but not 14 bit and
all of our Coolsnap HQ2's and our Andor xIon EMCCD cameras acquire in the 14
bit range (For the EMCCD cameras this is to do with how NIS handles them). What
I have to do is select 16 bit unsigned and then in the 'set option' enter the
14 bit range. EVERY TIME!!! Since I manage a facility of 200 users I'm sure the
reader can imagine how popular this is. If this pretty simple tweak could be
supported I would be most grateful.

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:
\\Mvm-igmm-h213\z$\FIJI-W~1\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => \\Mvm-igmm-h213\z$\FIJI-W~1\FIJI-W~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150319171059)
Fiji: http://fiji.sc/update/ (last check:20150319202456)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20150302220629)

Files not up-to-date:
  c3f8675e (OBSOLETE_UNINSTALLED) 20141216163551 jars/Jama.jar
  b6bf3817 (OBSOLETE_UNINSTALLED) 20141216163611 jars/edu_mines_jtk.jar
  986cfcf5 (OBSOLETE_UNINSTALLED) 20141216163621
jars/imglib2-algorithms-2.0.0-beta-26.jar
  ce6460d3 (OBSOLETE_UNINSTALLED) 20141216163621
jars/imglib2-algorithms-gpl-2.0.0-beta-26.jar
  673fae25 (OBSOLETE_UNINSTALLED) 20141216163621
jars/imglib2-algorithms-legacy-2.0.0-beta-26.jar
  51eadb2a (OBSOLETE_UNINSTALLED) 20141216163621
jars/imglib2-meta-2.0.0-beta-26.jar
  25895ad6 (OBSOLETE_UNINSTALLED) 20141216163622
jars/imglib2-ops-2.0.0-beta-26.jar
  8c636e50 (OBSOLETE_UNINSTALLED) 20141216163624 jars/jai_codec.jar
  717dd8e0 (OBSOLETE_UNINSTALLED) 20141216163625 jars/jai_core.jar
  1ad3be0d (LOCAL_ONLY) 20141216163637 jars/jpedalSTD.jar
  f416387c (LOCAL_ONLY) 20150223132413 plugins/SIMcheck-0.9.5.jar

-- 
You are receiving this mail because:
You are the assignee for the bug.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-bugs/attachments/20150323/268c7f6f/attachment.html>