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Bug 1081 - Unable to read images I was able to read in earlier versions
Unable to read images I was able to read in earlier versions
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-06-02 09:24 CDT by Gabriel Einsdorf
Modified: 2015-06-03 06:52 CDT
3 users (show)

See Also:

Description Gabriel Einsdorf 2015-06-02 09:24:14 CDT
The uploaded sample image: 
ARRAYSCANVTI_150316130001_A02f00d0.DIB 
is an image I was able to open perfectly in earlier versions of fiji (like two weeks ago). But this is no longer possible, I get the error "Not a BIP File"
I hope you can fix this soon.
Greetings Gabriel

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 4.0.4-1-MANJARO
  java.version => 1.7.0_80
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.7.0_80-b15
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 24.80-b11
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.7
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /usr/lib/jvm/java-7-jdk/jre
  imagej.dir => /home/gabriel/bin/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150602035708)
Fiji: http://fiji.sc/update/ (last check:20150601174046)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150530032643)
SCIFIO-dev: http://sites.imagej.net/SCIFIO/ (last check:20150529200112)
Comment 1 Mark Hiner 2015-06-02 09:33:20 CDT
Thanks Gabriel.

This sounds like a Bio-Formats problem, given that 5.1.2 was released last week.

You can download the 5.1.1 tools from the OME website[1] and test that they work with your file (e.g. by using the showinf tool)

If you can confirm that your file was supported in older versions of Bio-Formats, you should report the issue to the OME team[2].

Let me know if older BF versions don't work (and see also [3] for all downloads)

Best,
Mark

[1] http://downloads.openmicroscopy.org/bio-formats/5.1.1/
[2] https://www.openmicroscopy.org/site/support/bio-formats5.1/about/bug-reporting.html
[3] http://downloads.openmicroscopy.org/bio-formats/
Comment 2 Gabriel Einsdorf 2015-06-03 03:19:02 CDT
I was able to successfully open the files both with the command line tools of the 5.1.1 and the 5.1.2 versions of Bioformats. So there seems to be a problem with the Bioformats integration in imagej.
Comment 3 Curtis Rueden 2015-06-03 06:08:22 CDT
Gabriel, you probably turned off SCIFIO on the non-working installation.

Edit > Options > ImageJ2
Use SCIFIO when opening files (BETA!)

With that option on, I can open your file. With it off, it tries to use ImageJ1's I/O logic and reports the "Not a BMP file" error you mentioned.

Which version of BF you are using doesn't affect this.
Comment 4 Mark Hiner 2015-06-03 06:49:10 CDT
Thanks Curtis!
Comment 5 Gabriel Einsdorf 2015-06-03 06:52:39 CDT
(In reply to Mark Hiner from comment #4)
> Thanks Curtis!

Thanks Curtis!