[ome-users] Error: Plane index: 1 must be <1

[Roger Leigh]

On 08/05/14 10:32, Sabine Fischer wrote:
> Dear Bioformats team,
>
> I have a problem with the Bioformats command line tool.
>
> I want to extract individual z planes from Zeiss .czi files and
> according to the documentation the Bioformats command line tool
> bfconvert can be used for this. However, I can’t get this feature to
> work. I can convert a whole file from .czi to .tif but I cannot extract
> individual planes apart from the first one. I use the following code:
>
> bfconvert –z 1 “...\ZStack.czi” “...\converted.tiff”
>
> and as an error message I get
>
> “Plane index: 1 must be <1”
>
> (with –z 0 it works)
>
> Also if I try to use the patterns to save all z planes as individual
> files with the following code:
>
> bfconvert –z 1 ...\ZStack.czi ...\converted%z.tiff
>
> a file with the name convertedz.tiff is saved which contains all z planes.
>
> If I look at the metadata the zSize is recognised correctly and also if
> I use showinf.bat or the ImageJ plugin the file is read and displayed
> correctly.
>
> With the ImageJ plugin I can then also export the z planes as individual
> files.
>
> Ultimately, I want to do this conversion for large czi files (extracting
> time points, series and z planes) as part of a pipeline so I would
> prefer to use the command line tool not the ImageJ plugin.

Thanks for reporting this issue.  I can reproduce it with the current
5.0.1 release, and I've opened a ticket to track the issue
(http://trac.openmicroscopy.org.uk/ome/ticket/12268).  You should be CCd
on changes to the ticket, but if you'd prefer not to be, please let me
know and I'll remove your email address.


Thanks,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096