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Bug 312 - Overlay saved with image when save as JPEG and PNG but not save as TIFF
Overlay saved with image when save as JPEG and PNG but not save as TIFF
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2011-05-16 09:52 CDT by Andrew French
Modified: 2011-05-16 19:25 CDT
1 user (show)

See Also:

Attachments
Saving the overlay as a JPEG/TIFF (220 bytes, application/octet-stream)
2011-05-16 11:33 CDT, Andrew French

Description Andrew French 2011-05-16 09:52:49 CDT 
Hi
I added and overlay to an image, and saved it in various formats. The TIFF was missing the overlay.
Not sure which of these is expected behaviour but there is a difference.
Cheers


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

  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: You wanted never to be reminded.

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Fiji.app/java/win64/jdk1.6.0_24/jre
  fiji.dir => C:\Fiji.app

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Comment 1 G. Landini 2011-05-16 11:15:11 CDT 
Hi. I can save a tiff file with an overlay and retrieve it back, so I cannot reproduce in linux.
Can you please post a macro that shows it failing?
Comment 2 Andrew French 2011-05-16 11:33:33 CDT 
Created attachment 43
Saving the overlay as a JPEG/TIFF
Comment 3 Andrew French 2011-05-16 11:35:56 CDT 
Hi

OK so I wrote the macro and got the same behaviour.  HOWEVER, I noted that if I reload the TIFF in Fiji (rather than Photoshop as I was doing) the overlay is there. So I am guessing Fiji is saving it as a layer.  But Photoshop cannot see the layers, and ImageMagick seems to have problems with it. Is it saving a corrupt TIFF?

Thanks!
Andy
Comment 4 Andrew French 2011-05-16 11:38:42 CDT 
ImageMagick errors, if they are related: 
convert: Untitled.tif: unknown field with tag 50838 (0xc696) encountered. `TIFFReadDirectory' @ tiff.c/TIFFWarnings/703.
convert: Untitled.tif: unknown field with tag 50839 (0xc697) encountered. `TIFFReadDirectory' @ tiff.c/TIFFWarnings/703.

Version: ImageMagick 6.5.8-10 2010-12-17 Q16 http://www.imagemagick.org
Comment 5 Andrew French 2011-05-16 11:45:11 CDT 
Update:  I notice you can still turn on and off the overlay when reloaded in Fiji. So actually it must be saving it as a custom header in the TIFF?  That explains the behaviour, and IM errors.
Comment 6 G. Landini 2011-05-16 11:50:31 CDT 
TIFF is a tagged format, so if other software is not aware of the tag is, they should ignore the data. I think that this is what it might happening here.
To make sure you see it in other programs perhaps flattening the image is what you need?
The Overlay is not a Fiji exclusive feature, so maybe you could drop Wayne a line in case he is not reading this list.
Comment 7 Wayne Rasband 2011-05-16 19:25:08 CDT 
When saving in TIFF format, ImageJ uses the custom tags 50838 and 50839 to save the overlay in the TIFF header. Other applications ignore these tags so, to export images with overlays, you need to save in JPEG or PNG format, or you need to use the Image>Overlay>Flatten command and save as RGB TIFF.

-wayne