[ome-users] convert .czi file with bfconvert

[Roger Leigh]

On 15/08/14 12:00, Maier, Lorenz wrote:
> Dear Roger,
>
> sorry about the second command, apparently I've oversimplified.
>
> The command has to be
> bfconvert -channel 0 in.czi out_%%z.tif
>
>
> All files from _21.tif up to _40.tif seem to be corrupted.
>
> When loading with the bioformats plugin, Fiji reports:
> loci.formats.FormatException: loci.common.ReflectException: Cannot execute method: getNumPages
> (...)
> Caused by: java.lang.IllegalArgumentException: Bad endianness tag (not 0x4949 or 0x4d4d).
> (...)

Thanks, I've looked at this in some more detail.  This error is
legitimate; the images created by bfconvert are not valid TIFF files
after plane 20.  I have opened a separate ticket for this issue here and
CCd you on it:

   https://trac.openmicroscopy.org.uk/ome/ticket/12528


Regards,
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