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Bug 705 - file recognition
file recognition
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-02-20 09:32 CST by Marion Gröger
Modified: 2014-03-06 06:19 CST
4 users (show)

See Also:

Description Marion Gröger 2014-02-20 09:32:21 CST
if i use the new zeiss .czi* files, imagej as well as fiji is not able to read it.  i think that is or will be a problem for the whole zeiss community :-(
best
marion

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  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) 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.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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: D:\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => D:\Fiji.app

Information about the version of each plugin:

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Comment 1 Curtis Rueden 2014-02-20 16:58:45 CST
Please try enabling the "Bio-Formats 5" update site as described here:
   http://fiji.sc/Bio-Formats#Daily_builds

Several problems with CZI have been fixed in the past few months.

If you still have trouble reading your data, then please send a bug report to the Bio-Formats team on their mailing list:
https://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html

You will likely need to send them a sample nonworking CZI file.
Comment 2 Johannes Schindelin 2014-03-05 15:41:56 CST
Marion, any news?
Comment 3 Johannes Schindelin 2014-03-06 04:05:54 CST
On Thu, 6 Mar 2014, Marion Gröger wrote:

> no, i could find the imagej updater on my fiji surface. internet was also not
> helpful. :-( therefore i could not remove the bio-formats5 and have still the
> same problem than before. should i send a non readable file to the bioformats
> group?
> thanx for asking!
> marion

You probably meant that you could *not* find the updater. It is the "Update Fiji" entry in the "Help" menu (should be at the very bottom).

If in doubt, just hit Ctrl+L (or Command+L on MacOSX) just after starting Fiji, type "update" and then double-click the correct entry in the result list.

I also assume that you have *not* enabled the Bio-Formats 5 update site, and therefore do not want to *remove* it, but rather to enable it in your setup. You can do that by clicking on "Manage update sites" and checking the respective entry, then closing that dialog.

Having said that, I asked whether things are better now because the main Fiji update site just got Bio-Formats 5. You should therefore see the situation at least changed, maybe even improved, just by updating Fiji.
Comment 4 Jan Eglinger 2014-03-06 06:19:07 CST
Via mail:

On 06.03.2014, 11:42 AM, Marion Gröger wrote:
> i updated fiji and it works now!
> thanx a lot
> marion
>