TIFF stack import in ZEN

[Philip Nicovich]

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Has anyone had any luck correctly importing TIFF stacks into Zeiss ZEN
software?  Taking a multidimensional OME format TIFF file or ImageJ
hyperstack export and importing this into ZEN currently results in data
collapsed into a single-channel Z stack, regardless of timelapse or channel
information in the TIFF metadata.  These are files generated on TILL
Photonics instruments or even through ZEN's own OME TIFF export function.
I'm sure there's a straightforward way to do this correctly that someone
has done before!

Any help would be greatly appreciated!

Thanks,
Rusty Nicovich


--

*Philip R Nicovich*

*Research Fellow,  **ARC Centre of Excellence in Advanced Molecular Imaging*



THE UNIVERSITY OF NEW SOUTH WALES

UNSW  SYDNEY  NSW  2052  AUSTRALIA

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[Guiet Romain]

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Hi,

After seeing your e-mail I did a couple of test, using the « confocal-series.tif » (a z-stack, with 2 channels) available within the ImageJ samples package.

I saved it as « .tif », « ome.tif » and « ics » and try to open with Zen (lite 2012 BlackEdition and Lite 2012 BlueEdition).

I was able to open it using Zen Lite 2012 BlueEdition through this procedure:
In FIJI, export using BIO-Formats exporter as ome.tif, and tick all the options (ie. Write each … to a separate file)
In Zen Lite BlueEdition:
# File -> Export/Import -> Import (or menu Processing, in Method -> Export/Import -> Image Import)
# In Method Parameters:
Select MultiChannel
Select Z-stack
Select Sequential (instead of Automatic, automatic doesn’t allow to change value below)
File List, browse to your folder
Specify Prefix
Specify Z and C indexes
# Now, you can finally press Apply and get your image open as a z-stack with 2 channels

I tried on Zen 2012 BlackEdition and ZEN Lite 2012 BlueEdition. Surprisingly, none of them offer to import ics/ids file. We encounter this kind of issue using Imaris and exporting image with this file format was the easiest solution we found at that time.
All my other attempts gave as you observed a time-stack with consecutive channels and z-section.
I didn’t find in ZEN any tool to swap channel / slice / time , as it is possible to do in ImageJ/Fiji.

I hope it’ll help you,

Regards,

Romain


---------------------------------------------------------------
Dr. Romain Guiet
Bioimaging and Optics Platform (PT-BIOP)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Faculty of Life Sciences
Station 19, AI 0140
CH-1015 Lausanne

Phone: [+4121 69] 39629
http://biop.epfl.ch/
---------------------------------------------------------------

________________________________________
De : Confocal Microscopy List [[hidden email]] de la part de Philip Nicovich [[hidden email]]
Envoyé : mercredi 7 janvier 2015 05:44
À : [hidden email]
Objet : TIFF stack import in ZEN

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Has anyone had any luck correctly importing TIFF stacks into Zeiss ZEN
software?  Taking a multidimensional OME format TIFF file or ImageJ
hyperstack export and importing this into ZEN currently results in data
collapsed into a single-channel Z stack, regardless of timelapse or channel
information in the TIFF metadata.  These are files generated on TILL
Photonics instruments or even through ZEN's own OME TIFF export function.
I'm sure there's a straightforward way to do this correctly that someone
has done before!

Any help would be greatly appreciated!

Thanks,
Rusty Nicovich


--

*Philip R Nicovich*

*Research Fellow,  **ARC Centre of Excellence in Advanced Molecular Imaging*



THE UNIVERSITY OF NEW SOUTH WALES

UNSW  SYDNEY  NSW  2052  AUSTRALIA

T: [phone]

E: [hidden email] <[hidden email]>


CRICOS Provider No. 00098G