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

[Daniel White]

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, 5
> th, 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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