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

[Carnë Draug]

On 23 Sep 2014 14:26:02 -0500,  Melissa Linkert
<melissa at glencoesoftware.com> wrote:
> 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)?

Hi Melissa

I can confirm we were using version 5.0.4 of bioformats. We then
tried with the daily builds (by activating the Fiji update site of
Bioformats, and then building it from source (release 5.1.0-SNAPSHOT).

I have tried it again this morning with cset bb48c40.

Carnë