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

[Melissa Linkert]

Hi Ian,

> 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....

Thank you for the bug report.  I don't believe we have any data from the
GSD systems, so if you could upload one of the problematic files that
would be much appreciated.  I will be sending FTP instructions
privately, as it sounds like those files will be too large for our QA
system.

Before uploading, though, could you please confirm that your Fiji is up
to date ("Help > About Plugins > Bio-Formats Plugins" should show
version 5.0.4)?

Regards,
-Melissa

On Tue, Sep 23, 2014 at 07:43:05PM +0100, Ian Dobbie wrote:
> 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
> it.
> 
> 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. 
> 
> Thanks, 
> 
> Ian
> 
> -- 
> Ian Dobbie
> Micron Bioimaging Unit Manager,
> Biochemistry,
> University of Oxford,
> South Parks Road,
> Oxford
> OX1 3QU
> Tel: 01865 613323
> Email: ian.dobbie at bioch.ox.ac.uk
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