[ome-users] Issue in bfconvert command.

[Josh Moore]

Hi Mohanapriya

On Thu, Aug 9, 2018 at 5:32 PM, Narapareddy, Mohanapriya
<mohanapriya.narapareddy at emory.edu> wrote:
> I think u dont get my point correctly when i am trying to execute this
> command
>
>  bfconvert -bigtiff -compression LZW <input file.vsi> <outfile>-%s.tif
>
>
> its working fine in centOs , i am getting multiple image planes but when i
> am trying to execute in docker container i am getting only a single image
> plane. Please resolve this issue.

Sorry, for the confusion. I tested one of our VSI files, and multiple
series (70+) were generated both within and outside of Docker using
the openjdk:8 image. I think we're going to need some more information
to help you out:

 * What version of Java & Bio-Formats are you using in Docker?

 * How are you invoking bfconvert inside the docker container?

 * Can you show us your entire Dockerfile?

 * Are you seeing any warning messages or errors? Any non-0 exit codes?

Cheers,
~Josh



> Mohanapriya
>
> ________________________________
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of
> Riad Gozim (Staff) <r.gozim at dundee.ac.uk>
> Sent: Thursday, August 9, 2018 10:58:44 AM
>
> To: OME User Support List
> Subject: Re: [ome-users] Issue in bfconvert command.
>
>
> Hi Mohanapriya,
>
>
> Converting pyramidal levels to ome-tiff (if that's what you're looking for)
> is not possible at the moment, unfortunately.
>
>
> However, it is something we are working towards and will hopefully have
> support for converting soon.
>
>
> If you would like to follow our progress, you can find our design document
> here and the open pull requests here.
>
>
> Thanks
>
>
> Riad
>
> ________________________________
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of
> Narapareddy, Mohanapriya <mohanapriya.narapareddy at emory.edu>
> Sent: 08 August 2018 18:03:47
> To: OME User Support List
> Subject: Re: [ome-users] Issue in bfconvert command.
>
>
> I mean the pyramidal levels. Only the series 0 is converted from vsi to tiff
> format. Unable to convert other series levels
>
>
> Mohanapriya
>
> ________________________________
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of
> Riad Gozim (Staff) <r.gozim at dundee.ac.uk>
> Sent: Wednesday, August 8, 2018 12:18:38 PM
> To: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Issue in bfconvert command.
>
>
> Hi Mohanapriya,
>
>
> Could you clarify what you mean by "layers"? We're not sure if you mean
> subresolution/pyramidal levels, channels, or something else.
>
>
> Thanks,
>
> Riad
>
> ________________________________
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of
> Narapareddy, Mohanapriya <mohanapriya.narapareddy at emory.edu>
> Sent: 08 August 2018 16:37:39
> To: ome-users at lists.openmicroscopy.org.uk
> Subject: [ome-users] Issue in bfconvert command.
>
>
> Hello,
>
> when i try to convert the vsi file in to tiff file in the docker container,
> i am unable to convert all the layers of the vsi file properly. I just
> wanted to know whether the bfconvert command works properly in the docker
> container and also wanted to know how can i fix this issue.
>
>
> Mohanapriya