Bug 196 – Problem with coloured images in leica .lif files

Bug 196 - Problem with coloured images in leica .lif files


Summary:	Problem with coloured images in leica .lif files

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:	2010-07-19 12:20 CDT by ch-n
Modified:	2010-07-19 21:09 CDT
CC List:	1 user (show)

See Also:

Description ch-n 2010-07-19 12:20:43 CDT

Since the last update of the Bioformat/LOCI plugin that came with Fiji, it is impossible to open multicolour leica .lif files as composite/coloured images. Depending on your settings it either opens them with the images of the different colour channels alternating in the stack (default, XYCZT) or with all images of colour 1 first, then colour 2, then colour 3 and so on (XYZCT). This happens even when I explicitly tell it to use the "composite" colour mode in importer window.
Falling back to the old version fixes the problem, so it should be something introduced in the last update I installed, sometime last week.

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_20
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_20-b02-279-9M3165
  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 Johannes Schindelin 2010-07-19 12:51:23 CDT

Could you please upload a minimal example of the behavior via Help>Upload Sample Image?

Comment 2 ch-n 2010-07-19 13:56:23 CDT

I have just done so, the filename is M39-slice8-dirt.lif
In the top bar you will see that imageJ recognizes the two images as two colour channels (c:1/2 - Image009 and c:2/2 - Image009), however the lower bar is labeled "z", both images are shown with a green LUT and as z slices instead of different colours.

Comment 3 Curtis Rueden 2010-07-19 17:46:06 CDT

The Fiji version of Bio-Formats Importer is not the latest. Please try running "Plugins > LOCI > Update LOCI Plugins" and selecting either "trunk build" or "stable release" from the list, restarting Fiji, and then reading your data again. Please try with Hyperstack view mode, Default color mode and Autoscale enabled, and let us know how it goes.

Comment 4 ch-n 2010-07-19 19:30:07 CDT

Thanks for the help, I already tried the update, it does still not work when you use the Standard ImageJ-option but it works when using Hyperstack, Autoscale is not necessary.

Another more minor thing, in these newer versions that show the problems when using the Standard ImageJ-option, the loading bar is also gone when loading lifs which I find a step backwards, especially when you're loading a lot of data (5+GB) and want to see if the rest of the loading time is long enough to get some coffee...

Comment 5 Curtis Rueden 2010-07-19 21:08:30 CDT

Thanks for the quick feedback. It sounds like it is working for you with the Hyperstack view mode, so I'm closing the ticket. The "Standard ImageJ" view mode does not support one LUT per channel, and does not support Composite color mode. Originally I had removed the "Standard ImageJ" option completely because it has essentially no advantages, but a user complained. However, that user has since said his problems are resolved and he no longer needs the mode, so maybe I will remove it again, to avoid confusion.

Regarding the missing progress bar, this is a known recent bug—it was not removed on purpose. I tried once to track it down but it is elusive (on some machines the progress bar still works...). I have filed a bug in the Bio-Formats bug tracker and CCed you to keep you informed of any progress on the issue.

Comment 6 Curtis Rueden 2010-07-19 21:09:39 CDT

(In reply to comment #5)
> I have filed a bug in the Bio-Formats bug tracker

For those interested, the URL is:
http://www.loci.wisc.edu/trac/java/ticket/517