Bug 440 – cannot open lim images acquired with NIS element (Nikon)

Bug 440 - cannot open lim images acquired with NIS element (Nikon)


Summary:	cannot open lim images acquired with NIS element (Nikon)

Status:	RESOLVED MOVED

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:	2012-06-19 15:25 CDT by sylvie le guyader
Modified:	2013-07-07 10:44 CDT
CC List:	4 users (show)

See Also:

Attachments
cannot open lim images acquired with NIS element (Nikon) (347.09 KB, application/octet-stream) 2012-06-19 15:29 CDT, sylvie le guyader

Description sylvie le guyader 2012-06-19 15:25:23 CDT

get an error: file is not supported, a reader plugin is not available or was not found. 

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

  os.arch => x86
  os.name => Windows XP
  os.version => 5.1
  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) 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:\DOCUME~1\syle.AD\MYDOCU~1\Fiji.app/java/win32/jdk1.6.0_24/jre/
  ij.dir => C:\DOCUME~1\syle.AD\MYDOCU~1\Fiji.app

Information about the version of each plugin:

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  dc3a1bdd2b34edec84c29affaded489d0a22601d 20120509161438 luts/6_shades.lut
  0b3bbb6cf86adcb697c53c0277a12140966375dc 20120509161438 luts/Cyan Hot.lut
  655b55e6322c870632e5ff3156f002c0f5b893fe 20120509161438 luts/Green Fire Blue.lut
  2918f6d391ee38a4491163c30b4e75256a6633e7 20120509161438 luts/HiLo.lut
  a3312d3ff046120cccf5adcd400c512f78d18f93 20120509161438 luts/ICA.lut
  db5bf8a4e880d787d88f3273caf3db7ae6a5974f 20120509161438 luts/ICA2.lut
  9f7dd167f698970549ec20aa7d26b221ae7928f8 20120509161438 luts/ICA3.lut
  697dd3a4daf4abcd05cc4a79af3bcb3364fd0bb0 20120509161438 luts/Magenta Hot.lut
  524604de124b812940b02541a63516c84621237b 20120509161438 luts/Orange Hot.lut
  9c9a56c239e5d9c3262ace5124fff406cb3b831d 20120509161438 luts/Rainbow RGB.lut
  4e686ec669057c7de78497720bf52ebe00c3f8da 20120509161438 luts/Red Hot.lut
  2fdb7c96583f42348cd5cc789fba38dd6e349c89 20120509161438 luts/Thermal.lut
  321574916ccee56861ca6d581f6915cff5fe80e1 20120509161438 luts/Yellow Hot.lut
  a4cec22b96c306321ba4c7b3ff30df9fa7919616 20120509161438 luts/blue_orange_icb.lut
  c9e396a3f83ee8cebf1ed28d3e2d53296cc908e7 20120509161438 luts/brgbcmyw.lut
  60f85e63ba9a31fbb769ab32c75c22883df22883 20120509161438 luts/cool.lut
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Comment 1 sylvie le guyader 2012-06-19 15:29:19 CDT

Created attachment 65
cannot open lim images acquired with NIS element (Nikon)

Comment 2 Curtis Rueden 2012-06-19 19:25:43 CDT

If you use File > Import > Bio-Formats, you will see the real reason:

"loci.formats.UnsupportedCompressionException: Compressed LIM files not supported."

There is currently a ticket for it:
    http://trac.openmicroscopy.org.uk/ome/ticket/4091

But as the compression algorithm appears to be proprietary, it will probably not be supported soon. In the meantime, there may be an option in the acquisition software to turn off the compression.

Comment 3 Johannes Schindelin 2012-09-18 20:22:10 CDT

Should we close this as WONTFIX, then?

Comment 4 Curtis Rueden 2012-09-18 20:49:52 CDT

> Should we close this as WONTFIX, then?

It's up to you, based on what Fiji's policy is for long-term pending bugs. The bug is registered in the OME Trac with a milestone of "unscheduled" and I'm certain it won't be addressed for a long time. But "WONTFIX" implies we will *never* fix it, which is not necessarily the case here. Since the Fiji BugZilla does not let us note such information, it may be easiest to close it as "WONTFIX" even though that is not completely accurate. Or you could label it "MOVED" since the report is on the OME Trac too.

Comment 5 Johannes Schindelin 2013-07-07 09:26:05 CDT

As per Curtis' suggestion, I mark this 'moved'.