[ome-users] Issue opening Leica GSD lif files in bioformats.

Ian Dobbie ian.dobbie at bioch.ox.ac.uk
Tue Sep 23 19:43:05 BST 2014

Hi Everyone, 

I have found a rather annoying bug when opening .lif files from the
relatively new GSD system. We are trying to do two colour STORM and have
lif files with two extremely large time series (10,000 - 20,000 frames
each). Fiji copes fine with the first set of images but doesn't get the
second right. Additionally we seem to get extraneous data sets added to
the lif in the bioformats series options dialogue. 

Unfortunately this is on data from a demo session with the GSD so all we
have are the extremely large test data sets, 2GB +, although I'm pretty
sure size is not the issue. I can easily provide the data but I can
provide a smaller example, I'm sorry. 

According to the Leica LAS software the lif contains 10 entries, whereas
bioformats thinks there are 12 entries. Bioformats has repeated entries
for the extremely large image sets. Accessing the image sets produces the
following symptoms....

1) Selecting the first repeat of the first large image works fine.

2) The second repeat of the first large image set opens junk data. Some
regions appear to have diagonal stripes like it is trying to read data
with the wrong xy size, and probably starting at the wrong byte boundary.  

3) The first repeat of the second large image set, incorrectly has the
number of frames from the first large image set. If this is larger than
the real number of frames then you can open it, get reasonable data
until the end of the expected data and then junk. If the first image set
is smaller than the second then you truncate the image set when you open

4) opening later image sets which are labelled with the correct number of
frames fails, but I think that bioformats is trying to read beyond the end
of the lif file. 



Ian Dobbie
Micron Bioimaging Unit Manager,
University of Oxford,
South Parks Road,
Tel: 01865 613323
Email: ian.dobbie at bioch.ox.ac.uk

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