[ome-users] convert .czi file with bfconvert

[Maier, Lorenz]

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).
(...)

Best,
Lorenz

-----Ursprüngliche Nachricht-----
Von: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] Im Auftrag von Roger Leigh
Gesendet: Donnerstag, 14. August 2014 18:11
An: ome-users at lists.openmicroscopy.org.uk
Betreff: Re: [ome-users] convert .czi file with bfconvert

On 13/08/14 20:53, Maier, Lorenz wrote:

Dear Lorenz.

> There seem to be two errors with bfconvert 5.0.3 that occur for a .czi 
> file of X: 128, Y:128, C:2, Z:41.
>
> I've uploaded an example including input and commands at QA 9412.
>
> Command 1: bfconvert -z 1 in.czi out.tif
>
> Error:
>
> Exception in thread "main" loci.formats.FormatException: Plane index:2 
> must be < 2
>
>          at 
> loci.formats.FormatWriter.checkParams(FormatWriter.java:325)
>
>          at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:170)
>
>          at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:386)
>
>          at loci.formats.FormatWriter.saveBytes(FormatWriter.java:126)
>
>          at loci.formats.ImageWriter.saveBytes(ImageWriter.java:201)
>
>          at
> loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:547
> )
>
>          at
> loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:483)
>
>          at 
> loci.formats.tools.ImageConverter.main(ImageConverter.java:677)

This is an already open ticket for this error:
https://trac.openmicroscopy.org.uk/ome/ticket/12268?pane=edit
I've added you to this ticket.

> Command 2:
>
> bfconvert in.czi out_%%z.tif
>
> showinf out_40.tif
>
> Error:
>
> Exception in thread "main" loci.formats.FormatException:
> loci.common.ReflectException: Cannot execute method: getNumPages

I can't reproduce on Linux; I just get out_%nn.tif files created.  I'll try to reproduce on Windows this evening.


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 _______________________________________________
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