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Bug 892 - SCIFIO reads grayscale image stack as colored image
SCIFIO reads grayscale image stack as colored image
Status: ASSIGNED
Product: ImageJ
Classification: Unclassified
Component: SCIFIO
unspecified
PC Windows
: P3 normal
Assigned To: Mark Hiner
Depends on:
Blocks:
 
Reported: 2014-08-10 20:15 CDT by limjeremiah
Modified: 2015-04-06 15:49 CDT
3 users (show)

See Also:


Attachments
Grayscale image opening up as pseudo-colored stack (533 bytes, text/plain)
2014-08-10 20:15 CDT, limjeremiah

Description limjeremiah 2014-08-10 20:15:35 CDT
Created attachment 193
Grayscale image opening up as pseudo-colored stack

Hi, thank you for your help. I've discovered a bug where opening a known grayscale image using ImageJ2(SCIFIO) results in FIJI recognizing the image as a colored one. The images are acquired using a high speed monochromatic CCD sensor which is incapable of producing colored images. 

My temporary fix:
Tried converting to stack > hyperstack and specifying no color, that did not work too.
Ultimately, turning off SCIFIO helped in restoring normal functionality.

Thank you for your time. Feel free to contact me for further information.







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\limkh\DOCUME~1\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\limkh\DOCUME~1\FIJI-W~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140615084004)
Fiji: http://fiji.sc/update/ (last check:20140613070314)

Files not up-to-date:
  6348d2cf (LOCAL_ONLY) 20140807114026 plugins/LowpassFilters_.class
  e53b0aa8 (LOCAL_ONLY) 20140807162014 plugins/Macros/StartupMacros.fiji.ijm
Comment 1 Mark Hiner 2014-08-14 07:50:12 CDT
Just wanted to say thank you for the report and sample data.

You're doing precisely the right thing by disabling SCIFIO for now. We hope to resolve this issue soon!