[ome-users] Wrong metadata for Leica lif files in ImageJ

[Balaji Ramalingam (Staff)]

Hi,

Thank you for reporting your issue and submitting your file.
The issue was reproducible with the latest version of Bio-Formats(5.1.5) and I have created a ticket for the same,
https://trac.openmicroscopy.org/ome/ticket/13085#ticket
And you have been added to the cc list.

You will get notified once there is a status change on the ticket.

For future instances it would be great if you could submit your files to our QA server,
https://www.openmicroscopy.org/qa2/qa/upload/

Best,
Balaji

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Lingfeng Tang <lingfengtang1982 at gmail.com<mailto:lingfengtang1982 at gmail.com>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Wednesday, 28 October 2015 02:09
To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: [ome-users] Wrong metadata for Leica lif files in ImageJ


Hi all,



I have been doing timelapse imaging using Leica SP8 confocal for a while. After I got the lif file, I converted it to tiff files. Since the file is huge, we don't want to keep the original lif file. However, if I save the metadata file created by FiJi or FiJi2, it missed some important information, for example, the laser I used were 488 and 561 nm, but it only shows 633nm which I didn't use. Did anybody else experienced the same problem? Is there any way that can solve this problem?



Below is the information of my OS (windows 7), version of FIJI and java:


  os.arch => amd64

  os.name<http://os.name> => Windows 7

  os.version => 6.1

  java.version => 1.6.0_24

  java.vendor => Sun Microsystems Inc.

  java.runtime.name<http://java.runtime.name> => Java(TM) SE Runtime Environment

  java.runtime.version => 1.6.0_24-b07

  java.vm.name<http://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<http://java.vm.info> => mixed mode

  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment

  java.specification.name<http://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: UP_TO_DATE



I also attached the example lif file with wrong metadata, and the right metadata from Leica software.


Any ideas, suggestions will be appreciated!



Sincerely,

Lingfeng Tang

The University of Dundee is a registered Scottish Charity, No: SC015096
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