[ome-users] Issue in bfconvert command.

[Josh Moore]

On Fri, Aug 10, 2018 at 8:34 PM, Narapareddy, Mohanapriya
<mohanapriya.narapareddy at emory.edu> wrote:
> hello
>
> mohanapriya

Hi Mohanapriya,

did you intend to attach a file to this email? If so, I don't see one.

~Josh


________________________
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of
> Josh Moore <josh at glencoesoftware.com>
> Sent: Friday, August 10, 2018 6:39:58 AM
>
> To: OME User Support List
> Subject: Re: [ome-users] Issue in bfconvert command.
>
> 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