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<p style="margin-top:0;margin-bottom:0">hello</p>
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<p>mohanapriya</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of Josh Moore <josh@glencoesoftware.com><br>
<b>Sent:</b> Friday, August 10, 2018 6:39:58 AM<br>
<b>To:</b> OME User Support List<br>
<b>Subject:</b> Re: [ome-users] Issue in bfconvert command.</font>
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<div class="PlainText">Hi Mohanapriya<br>
<br>
On Thu, Aug 9, 2018 at 5:32 PM, Narapareddy, Mohanapriya<br>
<mohanapriya.narapareddy@emory.edu> wrote:<br>
> I think u dont get my point correctly when i am trying to execute this<br>
> command<br>
><br>
> bfconvert -bigtiff -compression LZW <input file.vsi> <outfile>-%s.tif<br>
><br>
><br>
> its working fine in centOs , i am getting multiple image planes but when i<br>
> am trying to execute in docker container i am getting only a single image<br>
> plane. Please resolve this issue.<br>
<br>
Sorry, for the confusion. I tested one of our VSI files, and multiple<br>
series (70+) were generated both within and outside of Docker using<br>
the openjdk:8 image. I think we're going to need some more information<br>
to help you out:<br>
<br>
* What version of Java & Bio-Formats are you using in Docker?<br>
<br>
* How are you invoking bfconvert inside the docker container?<br>
<br>
* Can you show us your entire Dockerfile?<br>
<br>
* Are you seeing any warning messages or errors? Any non-0 exit codes?<br>
<br>
Cheers,<br>
~Josh<br>
<br>
<br>
<br>
> Mohanapriya<br>
><br>
> ________________________________<br>
> From: ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of<br>
> Riad Gozim (Staff) <r.gozim@dundee.ac.uk><br>
> Sent: Thursday, August 9, 2018 10:58:44 AM<br>
><br>
> To: OME User Support List<br>
> Subject: Re: [ome-users] Issue in bfconvert command.<br>
><br>
><br>
> Hi Mohanapriya,<br>
><br>
><br>
> Converting pyramidal levels to ome-tiff (if that's what you're looking for)<br>
> is not possible at the moment, unfortunately.<br>
><br>
><br>
> However, it is something we are working towards and will hopefully have<br>
> support for converting soon.<br>
><br>
><br>
> If you would like to follow our progress, you can find our design document<br>
> here and the open pull requests here.<br>
><br>
><br>
> Thanks<br>
><br>
><br>
> Riad<br>
><br>
> ________________________________<br>
> From: ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of<br>
> Narapareddy, Mohanapriya <mohanapriya.narapareddy@emory.edu><br>
> Sent: 08 August 2018 18:03:47<br>
> To: OME User Support List<br>
> Subject: Re: [ome-users] Issue in bfconvert command.<br>
><br>
><br>
> I mean the pyramidal levels. Only the series 0 is converted from vsi to tiff<br>
> format. Unable to convert other series levels<br>
><br>
><br>
> Mohanapriya<br>
><br>
> ________________________________<br>
> From: ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of<br>
> Riad Gozim (Staff) <r.gozim@dundee.ac.uk><br>
> Sent: Wednesday, August 8, 2018 12:18:38 PM<br>
> To: ome-users@lists.openmicroscopy.org.uk<br>
> Subject: Re: [ome-users] Issue in bfconvert command.<br>
><br>
><br>
> Hi Mohanapriya,<br>
><br>
><br>
> Could you clarify what you mean by "layers"? We're not sure if you mean<br>
> subresolution/pyramidal levels, channels, or something else.<br>
><br>
><br>
> Thanks,<br>
><br>
> Riad<br>
><br>
> ________________________________<br>
> From: ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of<br>
> Narapareddy, Mohanapriya <mohanapriya.narapareddy@emory.edu><br>
> Sent: 08 August 2018 16:37:39<br>
> To: ome-users@lists.openmicroscopy.org.uk<br>
> Subject: [ome-users] Issue in bfconvert command.<br>
><br>
><br>
> Hello,<br>
><br>
> when i try to convert the vsi file in to tiff file in the docker container,<br>
> i am unable to convert all the layers of the vsi file properly. I just<br>
> wanted to know whether the bfconvert command works properly in the docker<br>
> container and also wanted to know how can i fix this issue.<br>
><br>
><br>
> Mohanapriya<br>
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