[ome-users] Issue in bfconvert command.

[Narapareddy, Mohanapriya]

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.


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<http://openmicroscopy.github.io/design/OME005/> and the open pull requests here<https://github.com/openmicroscopy/bioformats/pull/3189>.


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




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