[ome-users] Time series from Deltavision split into 4

[Melissa Linkert]

Hi Giovanni,

Thank you for sending the problematic file to the OME team.  We were
able to reproduce the problem, and have identified the necessary fix
as noted on our issue tracker:

https://trello.com/c/AdlH21K9/285-deltavision-file-incorrectly-reports-multiple-series

We will update that issue as progress is made on a fix.

Regards,
-Melissa

On Thu, Oct 4, 2018 at 10:52 AM Daniel White <dan at chalkie.org.uk> wrote:
>
> Hi Giovanni
>
> So you mean the file is only split up by bioformats if the
> . DV file is 2Gb or larger?
>
> Are yuu using a 64 bit operating system and 64 bit java? Or is there any 32 bit operating system or java involved.?
>
> You can upload a large file to the devs using the upload file gadget in the help menu of Fiji... Try that please?
>
> Best
>
> Dan
>
> On Thu, 4 Oct 2018, 09:47 Cardone, Giovanni, <cardone at biochem.mpg.de> wrote:
>>
>> Hi Dan,
>>
>>
>>
>> the experiment setup was very simple, no points or panels, just three channels (2 fluorescence and one brightfield).
>>
>> The ‘smallest’ DV file is about 2 GB, so I would need instructions on how to make it available.
>>
>>
>>
>> Thanks,
>>
>> Giovanni
>>
>>
>>
>>
>>
>> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Daniel White
>> Sent: Montag, 1. Oktober 2018 18:47
>> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
>> Subject: Re: [ome-users] Time series from Deltavision split into 4
>>
>>
>>
>> Hi Giovanni
>>
>>
>>
>> Sounds like a bug in the bioformats DV reader
>>
>>
>>
>> Please upload a small as possible DV file and matching log file to the bioformats team and then it will be possible to find and squash the bug.
>>
>>
>>
>> Did you use any advanced experiment t setup like points or panels?
>>
>> How many colour channels?
>>
>>
>>
>> Best
>>
>>
>>
>> Dan
>>
>> On Mon, 1 Oct 2018, 15:53 Cardone, Giovanni, <cardone at biochem.mpg.de> wrote:
>>
>> Hi,
>>
>>
>>
>> recently a user of the DeltaVision at our facility has experienced an issue with opening a .dv file in Fiji (bio-formats 5.9.2). Specifically, the series is made of 944 time points, three channels of 640x640 images. When trying to open it, it is split into four non sequential series of 236 time points each, generated by interleaving: first series contains 1st, 5th, 9th … time points, second series 2nd, 6th, 10th … time points, and so on.
>>
>> This issue appears randomly: for example, another series acquired the same day, 1024x1024 pixels, 3 channels, 560 time points, is properly opened as a single series.
>>
>> The software installed on the microscope computer has been recently updated to SoftWoRx 7.0.0 RC6.
>>
>> I tried to open the file with ICY, and the result is the same. The only software that we have and that could open it properly is Volocity 6.3.
>>
>> Did anyone else experience this problem?
>>
>>
>>
>> Thanks,
>>
>> Giovanni Cardone
>>
>>
>>
>> Imaging Facility
>>
>> Max Planck Institute of Biochemistry
>>
>> Martinsried, Germany
>>
>>
>>
>>
>>
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