[ome-users] Metadata issue with some LIF files

[Melissa Linkert]

Hi Niko,

> I've come across a problem using Bio-Formats to parse the metadata
> of some Leica LIF files. The dataset in question contains two sets
> of what Leica calls "Mark and Find" with seven Z-stacks each.
> 
> Using Bio-Formats to open the file with Fiji or Icy, I selected a
> single Z-stack and went on to check the metadata after loading had
> finished. I was particularly interested in the excitation
> wavelengths of the four channels but had to discover that both ch0
> and ch1 were listed as 488. As this was highly suspicious, I went to
> check the same file with the Leica LAS (light) software, finding ch0
> == 405 and ch1 == 488, which is what we expected.
> 
> To make things even more complicated, I used LAS to delete
> everything else but the stack in question from the dataset and saved
> it as a new LIF file. Opening this "cleaned" file with Bio-Formats
> is displaying the *correct* excitation values (ch0:405, ch1:488)!

Thanks for this - I can definitely reproduce the problem with the larger
file, but only with every other Z stack (starting with the second).  That
might explain why the smaller file doesn't have the same problem.

In any case, a ticket is now open:

http://trac.openmicroscopy.org/ome/ticket/12808

and as usual, you have been CC'd.

Regards,
-Melissa

On Thu, Mar 26, 2015 at 02:37:46PM +0100, Niko Ehrenfeuchter wrote:
> Dear all,
> 
> I've come across a problem using Bio-Formats to parse the metadata
> of some Leica LIF files. The dataset in question contains two sets
> of what Leica calls "Mark and Find" with seven Z-stacks each.
> 
> Using Bio-Formats to open the file with Fiji or Icy, I selected a
> single Z-stack and went on to check the metadata after loading had
> finished. I was particularly interested in the excitation
> wavelengths of the four channels but had to discover that both ch0
> and ch1 were listed as 488. As this was highly suspicious, I went to
> check the same file with the Leica LAS (light) software, finding ch0
> == 405 and ch1 == 488, which is what we expected.
> 
> To make things even more complicated, I used LAS to delete
> everything else but the stack in question from the dataset and saved
> it as a new LIF file. Opening this "cleaned" file with Bio-Formats
> is displaying the *correct* excitation values (ch0:405, ch1:488)!
> 
> Both files were uploaded (the original one as well as the cleaned
> one) to our university's file sharing service, alongside with the
> XML exported from Leica's LAS software when checking the properties
> of a dataset. I'm going to send the links to these files in a
> private message.
> 
> Best regards,
> ~Niko
> -- 
> Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum,
> University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
> Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch |
> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users