Bug 962 – 16 bit TIFFs fail in 1.49k with and without SCIFIO, worked in 1.47f

Bug 962 - 16 bit TIFFs fail in 1.49k with and without SCIFIO, worked in 1.47f


Summary:	16 bit TIFFs fail in 1.49k with and without SCIFIO, worked in 1.47f

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-11-19 17:48 CST by Frank
Modified:	2014-11-20 18:27 CST
CC List:	2 users (show)

See Also:

Attachments
16 bit tiff Zeiss SEM, works imagej 1.47v, fails 1.49b and 149k (1.51 MB, image/tiff) 2014-11-20 11:40 CST, Frank

Description Frank 2014-11-19 17:48:17 CST

I have been using ImageJ/Fiji to work with TIFF images from my Zeiss SEM. It can generate 8 or 16 bit TIFFs. The higher dynamic range is required for some quantitative image analysis.

I have used ImageJ/Fiji in the past with no problems. Version 1.47f with Java 1.6.0_24(32 bit) works fine on my 32 bit XP system. On my Win7 64 bit system, Version 1.49k, Java 1.6.0_24(64 bit) fails.

If the image is opened with SCIFIO on, the image is black, autoscale does nothing, and a histogram shows a range from 0 to 0.

If SCIFIO is disabled, the image displays, but the 16-bit unsigned grey scale is "wrapped around" and the autoscale fails to correct the display, however the histogram works, it correctly displays the min/max values (412 and 65010 in one case) with a reasonable-looking histogram covering this range.

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:\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Fiji\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141109231443)
Fiji: http://fiji.sc/update/ (last check:20141119150803)

Comment 1 Wayne Rasband 2014-11-19 20:31:11 CST

Please attach a TIFF that exhibits this problem.

Comment 2 Frank 2014-11-20 11:40:07 CST

Created attachment 221
16 bit tiff Zeiss SEM, works imagej 1.47v, fails 1.49b and 149k

Hello Wayne
Thanks for the quick response (and for image J!). I have attached a 16-bit unsigned TIF file generated by Zeiss SmartSEM software. This opens correctly with 1.47v from the download site, but fails with later versions - histogram is correct but image contrast seems to be lower 8 bits or wrapped around. With SCIFIO no display, histogram all zeros.
Regards, Frank

Comment 3 Wayne Rasband 2014-11-20 18:27:36 CST

This ImageJ 1.48 regression is fixed in the 1.49m7 daily build, or work around the problem by using the Image>Lookup Tables>Grays command, which restores the default grayscale LUT. The 16 bit Zeiss SEM image Frank uploaded has an invalid 256 entry LUT, which is ignored by the daily build.