Bug 232 – stall on opening OME TIFF with Bio-Formats

Bug 232 - stall on opening OME TIFF with Bio-Formats


Summary:	stall on opening OME TIFF with Bio-Formats

Status:	RESOLVED FIXED

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

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2010-09-04 18:29 CDT by James Ackman
Modified:	2011-03-23 15:23 CDT
CC List:	1 user (show)

See Also:

Description James Ackman 2010-09-04 18:29:31 CDT

Fiji (ImageJA 1.44f) stalls when trying to open an OME TIFF stack (2200 64x128 px frames). This happens whether the ome.xml file is drag and dropped on the Fiji GUI or whether I explicitly utilize the loci_tools.jar plugin throught the menu.  

In either case, the Bioimport Import Options window correctly pops up, but when clicking 'OK' and progressing past this point the Fiji menu bar displays 'Parsing XML' then flashes between the messages 'Checking comment style' and 'Populating Metadata' infinitely (for at least as long as I checked--2minutes) while utilizing 130-190% of CPU on my Core2Duo MacBookPro.  This behavior persists with both the lastest stable and daily builds of loci_tools.jar. 

However, the same OME TIFF stack opens up just fine (within 10sec) under ImageJ64 1.43u java 1.6.0_20 with loci_tools.jar on the same machine.

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 => 10.6.4
  java.version => 1.6.0_20
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_20-b02-279-10M3065
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 16.3-b01-279
  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 => /

Comment 1 Curtis Rueden 2010-09-11 00:38:40 CDT

Thanks for the bug report, James.

There are currently a number of issues with reading OME-TIFF in the latest builds of Bio-Formats. We will look into it and reply back to this ticket with more information within 2-3 weeks.

Just to clarify: with Fiji/ImageJA v1.44f and the latest trunk build of loci_tools.jar you experience the stalling, but with Fiji/ImageJA v1.43u and the latest trunk build of loci_tools.jar you do not?

Also, I am surprised that dragging and dropping a .ome.tif file onto the Fiji GUI pops up the Bio-Formats window. The behavior I see is that ImageJ's default TIFF logic takes over and opens it that way.

Comment 2 James Ackman 2010-09-29 18:10:17 CDT

I didn't try it with Fiji/ImageJA v1.43u, but it does work just fine with native installation of ImageJ v1.43u. 

Drag/drop behavior is the same for me, drag/drop of an ome.xml file on the GUI opens bioformats, but drag/drop of an ome.tif on the GUI utilizes ImageJ's default TIFF logic. 

Here is some more recent information on opening a 1000 frame OME TIFF stack using Bio-Formats importer:
Fiji/ImageJA 1.44h:  stack opens, taking 45.62 seconds. 'Checking comment style' and 'Populating Metadata' flashed repeatedly during each frame as it opens.
ImageJ 1.43u:  stack opens in only 7.84 seconds.  'Checking comment style' and
'Populating Metadata' seemingly flashed only at first frame.   

Seems like there is an extra loop somewhere slowingly things down in the Fiji/loci_tools installation.  So I don't know if this is a Bio-formats bug or a Fiji/ImageJA bug, I'll update my native ImageJ installation to 1.44h and test the latest Bio-Formats and if I find anything I'll let you know.






(In reply to comment #1)
> Thanks for the bug report, James.
> 
> There are currently a number of issues with reading OME-TIFF in the latest
> builds of Bio-Formats. We will look into it and reply back to this ticket with
> more information within 2-3 weeks.
> 
> Just to clarify: with Fiji/ImageJA v1.44f and the latest trunk build of
> loci_tools.jar you experience the stalling, but with Fiji/ImageJA v1.43u and
> the latest trunk build of loci_tools.jar you do not?
> 
> Also, I am surprised that dragging and dropping a .ome.tif file onto the Fiji
> GUI pops up the Bio-Formats window. The behavior I see is that ImageJ's default
> TIFF logic takes over and opens it that way.
>

Comment 3 Curtis Rueden 2010-10-11 18:25:30 CDT

Would you mind testing again with the latest loci_tools.jar trunk build? If the issue persists, it would be helpful to have a sample OME-TIFF file demonstrating the problem, so that we can reproduce here. Thanks!

Comment 4 Johannes Schindelin 2011-03-23 15:23:30 CDT

Assuming that this has been fixed in the meantime. If not, please reopen with more information.