Bug 883 – File->Open mis-reads Gatan DM3 files

Bug 883 - File->Open mis-reads Gatan DM3 files


Summary:	File->Open mis-reads Gatan DM3 files

Status:	ASSIGNED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	Mark Hiner

URL:

Depends on:
Blocks:

Reported:	2014-08-06 14:29 CDT by Steven Cogswell
Modified:	2014-09-04 11:36 CDT
CC List:	3 users (show)

See Also:

Attachments
DM3 Image, 16-bit, 1024x1024 px, 2.27x2.27 um (2.16 MB, application/octet-stream) 2014-08-06 14:46 CDT, Steven Cogswell

Description Steven Cogswell 2014-08-06 14:29:36 CDT

Opening a Gatan Digital Micrograph .dm3 format file from the "File" -> "Open" menu will result in a black image with incorrect spatial calibrations (units are incorrect under "set scale").   "File" -> "Import" -> "DM3 Reader" works correctly, as does dragging the file in the finder onto the Fiji icon.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140802115300)
Fiji: http://fiji.sc/update/ (last check:20140730150634)

Files not up-to-date:
  673486c6 (LOCAL_ONLY) 20130510132501 plugins/ExtendedDepthField.txt
  0a5c1981 (LOCAL_ONLY) 20130531132531 plugins/steve/Color_Profiler.jar

Comment 1 Mark Hiner 2014-08-06 14:38:37 CDT

Hi Steven,

There are two things that I would like you to try:

1) Opening your data with "File > Import > Bio-Formats".
If this fails, then the issue is probably with Bio-Formats and you should submit a bug using their issue tracking guidelines: http://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html

2) Opening again with "File > Open", but once with "Edit > Options > ImageJ2... > Use SCIFIO when opening files" enabled, and once disabled.

If the Bio-Formats importer test looks good, but it fails with SCIFIO, then please upload your .dm3 dataset either as an attachment here, or via "Help > Upload Sample Image" if you would like the data to remain private. That will allow us to reproduce the issue and investigate further.

Thanks!

Comment 2 Steven Cogswell 2014-08-06 14:46:38 CDT

Created attachment 191
DM3 Image, 16-bit, 1024x1024 px, 2.27x2.27 um

This image is just some boring horizontal grey lines from a Gatan camera with noise issues.

Comment 3 Steven Cogswell 2014-08-06 14:49:23 CDT

Hello;

Bug report was done with SCFIO enabled

1. Import with Bioformats shows a black image with correct scale (um), but image looks okay after using auto brightness/contrast.  This is with SCIFIO enabled. 

2. with SCIFIO disabled File-Open shows the image as expected, with proper brightness contrast, and proper scale (um).  

I've uploaded an image I was using to test, which is not exciting but shows the import issues.  

Best regards,
Steven Cogswell

Comment 4 Mark Hiner 2014-08-06 14:57:59 CDT

Thanks for the report, and for the quick response!

It looks like SCIFIO is opening the same data as Bio-Formats (which it should be), as it looks the same after running Brightness/Contrast, but the calibration data is lost along the way.

Probably not DM3 specific, but a bug in the use of calibration in https://github.com/scifio/scifio-bf-compat