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Bug 758 - FIJI does not open .lsm files anymore
FIJI does not open .lsm files anymore
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-05 17:43 CDT by Steve J. West
Modified: 2014-06-10 14:13 CDT
3 users (show)

See Also:


Attachments
.lsm image with two channels (1.95 MB, image/tiff)
2014-06-06 07:24 CDT, Steve J. West

Description Steve J. West 2014-06-05 17:43:16 CDT
Hi,

I recently updated FIJI, and now I cannot open .lsm 5 files from zeiss confocal images.

Initially, FIJI says the following:

"Initialising [filename]"

Then it states:

"Computing min/max complete"

But no image opens.  I have tried using the import function in the file menu, but this does not work either.

Thanks, any help with this problem would be hugely appreciated.

Best,

Steve West.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.2.0-4-amd64
  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.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  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: /home/sjwest/Documents/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/sjwest/Documents/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140605164707)
Fiji: http://fiji.sc/update/ (last check:20140603162429)

Files not up-to-date:
  9867e817 (LOCAL_ONLY) 20140310142353 plugins/3D_Shape.jar
  0e8ddb6d (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/arpack-combo.jar
  1a08e201 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/csparsej.jar
  924b8d62 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/jplasma.jar
  fca468e8 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/jtransforms.jar
  dd8c3801 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/licenses/parallelcolt.LICENSE.txt
  de89ab4e (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/licenses/paralleliterativedeconvolution.LICENSE.txt
  60508fb7 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/macros/ParallelIterativeDeconvolution2D.txt
  20e21511 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/macros/ParallelIterativeDeconvolution3D.txt
  89cb5823 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/netlib-java.jar
  25802519 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/optimization.jar
  33f69ff8 (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/parallel_iterative_deconvolution-1.12.jar
  87fc836e (LOCAL_ONLY) 20130919181544 plugins/ParallelIterativeDeconvolution/parallelcolt-0.9.4.jar
  630864de (LOCAL_ONLY) 20140310142235 plugins/Resize_.jar
Comment 1 Johannes Schindelin 2014-06-05 19:19:21 CDT
I hope to find some time tomorrow to work on this; Could you -- in preparation for my bug hunt -- upload the .lsm via Help>Upload Sample Image? Thank you!
Comment 2 Steve J. West 2014-06-06 07:24:21 CDT
Created attachment 156
.lsm image with two channels
Comment 3 Steve J. West 2014-06-06 07:27:09 CDT
Hi Johannes,

OK - I will attach a small .lsm file with two channels for you to help with your bug hunt!

I have just restarted my computer, and it seems to be opening .lsm files again.  But the problem now is that .lsm files which contain more than one channel is no longer recognised as actually having more than one channel.

The multichannel image will open, but each "channel" is the same colour, and commands that work with multichannel images do not work.

For example, I can open the .lsm, but if I try to run the "Split Channels" or the "Reduce Dimensionality" commands, they return an error such as "multichannel image required", or a NullPointerException, respectively.

FIJI also seems to be constantly loading the image even after it has been opened, and after closing the image, it is still present under the Window File menu.

Thanks, any help would be great!

Steve.
Comment 4 Steve J. West 2014-06-06 08:38:44 CDT
Quick update;

I removed all of the files that were updated last night, and have added them one by one back into the jars folder in FIJI.  Once I removed all of the updates, and re-added them one by one, I have found that it is the scijava-common-2.22.3.jar file that is causing FIJI to open the .lsm files incorrectly.

With the scijava-common-2.22.3.jar file removed, FIJI can open a .lsm and recognise the channels perfectly.  So I presume the bug is in this file?

Sorry, Im not an expert in Java programming, but hopefully this information might help with the bug fix!

Cheers,

Steve.
Comment 5 Johannes Schindelin 2014-06-06 09:02:28 CDT
Nice analysis! Unfortunately, it is as with knockout experiments: it is hard to figure out whether you knocked out the vital part, or some support chain for the vital part of the function you wanted to study.

In this case, scijava-common is simply required for SCIFIO to work. By "knocking out" scijava-common, SCIFIO was knocked out, but also *all* of ImageJ2. You probably saw that the window title is no longer "(Fiji Is Just) ImageJ", but instead "ImageJ". Basically, you downgraded to a plain ImageJ 1.x.

For the time being (sorry for not stating this clearly and earlier) there is an easier work-around that will not break many other things: just go to Edit>Options>ImageJ2 and click off "Use SCIFIO". This will fall back to the previous method of opening files.

We will be busy fixing this bug, of course, and hopefully have something to show to you (and for you to test, please) by the end of the day.
Comment 6 Steve J. West 2014-06-06 09:59:49 CDT
Thanks for the update!  Yes, I suppose this also would explain why it is hard to interpret most KO studies as well?  As in any complex system with many interacting components, there will be many knock-on effects!

I did have a quick read online of what scijava-common is, and it appears to be a library of some kind, so I was a little suspicious that it would actually be the root cause...

OK - have unchecked the SCIFIO option, and it is working now.

Sure, happy to test any bug fixes!  Thanks for all your help.

Steve.
Comment 7 Mark Hiner 2014-06-09 12:02:09 CDT
Hi Steve,

>The multichannel image will open, but each "channel" is the same colour, and 
>commands that work with multichannel images do not work.

As a workaround, I just wanted to point out that you can run Image > Color > Make Composite, or use the Channels Tool to convert your image to a composite image.

This will allow you to view your data via the composite mode you're used to.
Comment 8 Mark Hiner 2014-06-10 14:13:02 CDT
With the latest Fiji release, we updated how Composite and RGB images are created. This dataset actually now opens in composite mode now and should behave more like you were used to.

Some users may still have data that opens in RGB mode by default, when they expected composite, in which case the above workaround of converting to composite mode should still work (if it doesn't, please report as a bug).