Bug 258 – Opening multiposition LSM files by Drag&Drop throws exception

Bug 258 - Opening multiposition LSM files by Drag&Drop throws exception


Summary:	Opening multiposition LSM files by Drag&Drop throws exception

Status:	RESOLVED FIXED

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

Importance:	P2 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2010-12-07 14:16 CST by Jan Eglinger
Modified:	2011-04-13 18:42 CDT
CC List:	0 users

See Also:

Attachments
Multiposition (4p) multichannel (3c) LSM file scanned with Zeiss LSM 710 (2.34 MB, application/x-zip) 2011-04-04 13:44 CDT, Jan Eglinger

Description Jan Eglinger 2010-12-07 14:16:54 CST

I tried opening a Zeiss LSM file acquired with the multi-position mode in ZEN2010 software. The LSM_Reader (after Drag&Drop) throws the following exception, while opening via Plugins > LOCI > Bio-Formats Importer works fine with the latest release (4.2.2) of Bioformats.

(tried on a MacOS 10.5 with up-to-date Fiji)
I can upload a 3.5MB example lsm file if required.

Cheers,
Jan

java.lang.IllegalArgumentException: channels<2 or stacksize not multiple of channels
	at ij.CompositeImage.<init>(CompositeImage.java:65)
	at org.imagearchive.lsm.reader.Reader.readStack(Reader.java:688)
	at org.imagearchive.lsm.reader.Reader.open(Reader.java:509)
	at org.imagearchive.lsm.reader.Reader.open(Reader.java:97)
	at org.imagearchive.lsm.reader.Reader.open(Reader.java:47)
	at LSM_Reader.run(LSM_Reader.java:46)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.IJ.runPlugIn(IJ.java:143)
	at HandleExtraFileTypes.tryPlugIn(HandleExtraFileTypes.java:370)
	at HandleExtraFileTypes.tryOpen(HandleExtraFileTypes.java:169)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:332)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:52)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.IJ.runPlugIn(IJ.java:143)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:412)
	at ij.io.Opener.openImage(Opener.java:289)
	at ij.io.Opener.openImage(Opener.java:308)
	at ij.io.Opener.open(Opener.java:142)
	at ij.io.Opener.openAndAddToRecent(Opener.java:228)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:182)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:158)
	at java.lang.Thread.run(Thread.java:680)


***************************************************************

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

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.5.8
  java.version => 1.6.0_22
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_22-b04-307-9M3263
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 17.1-b03-307
  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: Up-to-date

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2010-12-07 17:12:40 CST

Jan, would you suggest to make LOCI the default opener for .lsm files?

Comment 2 Jan Eglinger 2010-12-07 17:43:30 CST

(In reply to comment #1)
> Jan, would you suggest to make LOCI the default opener for .lsm files?
> 
Now that you ask, I think that would be a sensible solution. (loci_tools seems to be more actively developed than the LSM_Reader, doesn't it?)

My only concern is that LOCI currently doesn't recognize the correct channel colorization in these LSM files (correct me if I'm wrong).

Comment 3 Curtis Rueden 2010-12-07 19:13:40 CST

(In reply to comment #2)
> My only concern is that LOCI currently doesn't recognize the correct channel
> colorization in these LSM files (correct me if I'm wrong). 

If you have sample data demonstrating any deficiencies in the Bio-Formats LSM support, we would love to get a copy so that we can fix the issue!

Comment 4 Jan Eglinger 2010-12-07 19:39:19 CST

(In reply to comment #3)
> If you have sample data demonstrating any deficiencies in the Bio-Formats LSM
> support, we would love to get a copy so that we can fix the issue!
>
Thanks Curtis,

I've just sent an example file by mail concerning this issue.

Comment 5 Johannes Schindelin 2011-03-23 14:57:55 CDT

This was fixed, correct?

Comment 6 Jan Eglinger 2011-04-04 13:39:59 CDT

(In reply to comment #5)
> This was fixed, correct?
> 

Not fully yet, I'm afraid.

The exception is gone when opening multiposition stacks, but with the current LSM_Reader.jar, the lsm file opens as a simple stack (12 slices in my case), whereas the "locally modified" LSM_Reader that I had installed before (v4.0g sent from Jerome Mutterer) was opening it as a hyperstack (3c,4t).

I'll upload the example file.

Comment 7 Jan Eglinger 2011-04-04 13:44:35 CDT

Created attachment 37
Multiposition (4p) multichannel (3c) LSM file scanned with Zeiss LSM 710

The attached file (please unzip first) should open as a 4-position, 3-channel hyperstack in Fiji.

Comment 8 Wayne Rasband 2011-04-04 20:06:16 CDT

The LSM Reader included with ImageJ 1.44 (v4.0g) and also available at

    http://rsb.info.nih.gov/ij/plugins/lsm-reader.html

open the example file as  a 4-position, 3-channel hyperstack.

-wayne

Comment 9 Johannes Schindelin 2011-04-04 23:31:41 CDT

I pushed the changes to the 'lsm-reader-4.0g' branch, and hope to merge to 'master' and to upload to the Updater soon.

Comment 10 Curtis Rueden 2011-04-08 21:35:54 CDT

Just to follow up on the Bio-Formats side of things, the color issue Jan mentioned was fixed a while back; see this ticket: http://dev.loci.wisc.edu/trac/software/ticket/617

Comment 11 Johannes Schindelin 2011-04-13 18:42:28 CDT

I just uploaded version 4.0g of the LSM Reader, which should fix the issue.