[OpenSPIM] Input data for SPIM Registration PlugIn

[Selchow, Olaf]

Dear Kieran and Ricarda,

To my knowledge, the export of .czi data from the ZEISS Lightsheet Z.1 should be not necessary any more.
The .czi data  can be read directly by Bioformats reader into Fiji …

Kevin Eliceiri and Stephan Preibisch are the experts in this …

Pls let me know if I can help in that data from ZEISS microscopes can be opened in the software where you need it.

With best regards,
Olaf

__________________________

Carl Zeiss Microscopy GmbH
Geschäftsbereich BioSciences / BioSciences Division
Produktmanager / Product Manager

D r.   O l a f   S e l c h o w

Carl-Zeiss-Promenade 10, 07745 Jena
Telefon/Phone: +49 3641 64-2089
Cell Phone: +49 151 4615 8629
Fax: +49 3641 64-3144
mailto:olaf.selchow at zeiss.com
http://www.zeiss.com/microscopy

__________________________

Carl Zeiss Microscopy GmbH
Vorsitzender des Aufsichtsrates: Dr. Michael Kaschke
Geschäftsführung: Dr. Ulrich Simon, Wilhelm Nörthemann, Dr. Frank Stietz
Sitz der Gesellschaft: 07740 Jena, Deutschland
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Von: openspim-bounces at openspim.org [mailto:openspim-bounces at openspim.org] Im Auftrag von Kieran Short
Gesendet: Dienstag, 27. Mai 2014 23:19
An: Shugi at gmx.de
Cc: openspim at openspim.org
Betreff: Re: [OpenSPIM] Input data for SPIM Registration PlugIn

Richard,

The endianness of the TIFF data might be wrong (wrong byte order). Try switching to intel-byte order (or if it already is, switch it to big endian).

fyi: http://en.wikipedia.org/wiki/Endianness

cheers,
Kieran

On Tue, May 27, 2014 at 8:19 PM, <Shugi at gmx.de<mailto:Shugi at gmx.de>> wrote:
Hello,

I read about your tool for registration and fusion of multiple view images. It is the topic of my intership to find a way doing this with our data and I would like to try your tool. But it seems to have a problem with our data. The original data from a Z1 are present as czi file. I extract them as ome.tif file with the ZEN2012 Software. Like in the tutorial the extension was changed from ome.tif to tif. I was following the tutorial and when to interactivlly choosing the threshold for the beads and click "Done" the following Messages occure in the Log:

Opening first image to determine z-stretching.
Cannot open fie: ...

The path and the filename are correct. Maybe it is something about the formate? Do you need special tags in the tiff file or does the bit depth has influence?
Hope you can help me, because your tool seems to be very promising.

Kind regardas
Ricarda Bräuniger

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