[ome-users] Metadata issue with some LIF files

[Niko Ehrenfeuchter]

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