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Bug 437 - 48-bit tif format problem
48-bit tif format problem
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2012-06-12 13:51 CDT by Jean Livet
Modified: 2013-07-08 10:41 CDT
3 users (show)

See Also:
Description Jean Livet 2012-06-12 13:51:23 CDT 
Following Fiji updates in the last weeks, i noticed a minor bug occuring on two different systems (Windows 32bit and 64bit) with color images:
After making a 3 channel composite using the 'merge channel' tool, Fiji  improperly saves this image as a 48-bit color tif .
48-bit tif images generated in this way can be opened as color images with Fiji itself, but not other with other programs such as Photoshop. Instead Photoshop only sees the 1st channel and opens it as a 16-bit black and white image.

Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => x86
  os.name => Windows Vista
  os.version => 6.0
  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) Client 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: C:\Fiji.app/java/win32/jdk1.6.0_24/jre/
  ij.dir => C:\Fiji.app

Information about the version of each plugin:

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Comment 1 Wayne Rasband 2012-06-12 17:07:23 CDT 
3 channel 16-bit composite color images are saved as Photoshop-compatible 48-bit RGB TIFFs if the slice label of the first channel is "Red". You can set the slice label and save the image in a macro using

   setSlice(1);
   setMetadata("label", "Red");
   saveAs("tiff", "");

-wayne
Comment 2 Jean Livet 2012-06-12 19:45:05 CDT 
Thanks for your prompt reply. Using the suggested macro works.
However, should not the "Merge Channels" tool always create Composites where the first channel is red, thus enabling Photoshop-compatible saving without resorting to a macro (as was  the case before the Fiji update)?
-jean

(In reply to comment #1)
> 3 channel 16-bit composite color images are saved as Photoshop-compatible
> 48-bit RGB TIFFs if the slice label of the first channel is "Red". You can set
> the slice label and save the image in a macro using
> 
>    setSlice(1);
>    setMetadata("label", "Red");
>    saveAs("tiff", "");
> 
> -wayne
>
Comment 3 Johannes Schindelin 2013-07-07 09:49:53 CDT 
Closing due to inactivity.
Comment 4 Johannes Schindelin 2013-07-08 09:54:55 CDT 
Olivier, please feel free to open a different ticket for the remaining issue, or to provide additional information that helps resolve Jean's problem. However, from the inactivity it is quite obvious to me that Wayne will not change the behavior of ImageJ 1.x because the modification that triggered this bug report was most likely fully intended.

So let's only reopen this if and only if there is any prospect that the issue can be resolved with anything else than the macro suggested by Wayne.
Comment 5 olivier bardot 2013-07-08 10:41:20 CDT 
Sorry for that. I did not want to reopen this bug 437.