Re: TIFF stack import in ZEN (commercial response)

[Sebastian Rhode-2]

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Hi guys,

it is true, that our ZEN software is not perfectly suited for importing OME-TIFF data.
Especially there are still differences between ZEN Blue and Black.
One reason why this feature had not the highest priority in the past, was the "unclear"
use case. Most people open the CZI file directly in Fiji or use the OME-TIFF export from
ZEN. But usually the images "never" come back to ZEN.

Why do you want to re-import those images? If there is an increasing need for such re-
imports, this info is really helpful for me.

Cheers

Sebastian

Carl Zeiss Microscopy GmbH
Business Unit BioSciences
Software Product Management Widefield Research
Product Manager – Advanced Automated Analysis and Imaging Automation



On Wed, 7 Jan 2015 07:31:13 +0000, Guiet Romain <[hidden email]> wrote:

>*****
>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.
>*****
>
>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:
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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

[Csúcs Gábor-3]

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*****

Dear Sebastian,

I have used to do some image processing/visualization with the Zen/Zeiss
software even if the images were not acquired with a Zeiss microscope. In
the "old times" (before Zen) I was even able directly import Leica .tif
files in the Zeiss software. As I see it, lately Zeiss put quite some
effort to improve the analysis functionality of Zen. If someone has an
off-line Zen license, why not use it to analyze images from other systems?
Such a scenario may not be typical for a single lab, but quite common for
a core-facility.

Greetings     Gabor



On 1/13/15 9:33 AM, "Sebastian Rhode" <[hidden email]> wrote:

>*****
>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.
>*****
>
>Hi guys,
>
>it is true, that our ZEN software is not perfectly suited for importing
>OME-TIFF data.
>Especially there are still differences between ZEN Blue and Black.
>One reason why this feature had not the highest priority in the past, was
>the "unclear"
>use case. Most people open the CZI file directly in Fiji or use the
>OME-TIFF export from
>ZEN. But usually the images "never" come back to ZEN.
>
>Why do you want to re-import those images? If there is an increasing need
>for such re-
>imports, this info is really helpful for me.
>
>Cheers
>
>Sebastian
>
>Carl Zeiss Microscopy GmbH
>Business Unit BioSciences
>Software Product Management Widefield Research
>Product Manager ­ Advanced Automated Analysis and Imaging Automation
>
>
>
>On Wed, 7 Jan 2015 07:31:13 +0000, Guiet Romain <[hidden email]>
>wrote:
>
>>*****
>>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.
>>*****
>>
>>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 Š 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 doesn¹t 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 didn¹t find in ZEN any tool to swap channel / slice / time , as it is
>possible to do in
>ImageJ/Fiji.
>
>I hope it¹ll 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

[Steffen Dietzel]

*****
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.
*****

I second that. Either there is good image processing and analysis
capacity or there isn't. If there is anything that is beyond the
features of Fiji, you will want to use it with images from any source.
In particular if available with an off-line license. And ome.tiff seems
to be the closest thing to a standard format we have in microscopy.

I guess it comes down to the questions of whether the manufacturer
regards the image processing and analysis features in the software as
just a potentially-nice-to-have add-on to the microscope or as a serious
imaging package which works (more or less) independently of the source
of the images.

Steffen

Am 13.01.2015 um 13:41 schrieb Csúcs Gábor:

> *****
> 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.
> *****
>
> Dear Sebastian,
>
> I have used to do some image processing/visualization with the Zen/Zeiss
> software even if the images were not acquired with a Zeiss microscope. In
> the "old times" (before Zen) I was even able directly import Leica .tif
> files in the Zeiss software. As I see it, lately Zeiss put quite some
> effort to improve the analysis functionality of Zen. If someone has an
> off-line Zen license, why not use it to analyze images from other systems?
> Such a scenario may not be typical for a single lab, but quite common for
> a core-facility.
>
> Greetings     Gabor
>
>
>
> On 1/13/15 9:33 AM, "Sebastian Rhode" <[hidden email]> wrote:
>
>> *****
>> 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.
>> *****
>>
>> Hi guys,
>>
>> it is true, that our ZEN software is not perfectly suited for importing
>> OME-TIFF data.
>> Especially there are still differences between ZEN Blue and Black.
>> One reason why this feature had not the highest priority in the past, was
>> the "unclear"
>> use case. Most people open the CZI file directly in Fiji or use the
>> OME-TIFF export from
>> ZEN. But usually the images "never" come back to ZEN.
>>
>> Why do you want to re-import those images? If there is an increasing need
>> for such re-
>> imports, this info is really helpful for me.
>>
>> Cheers
>>
>> Sebastian
>>
>> Carl Zeiss Microscopy GmbH
>> Business Unit BioSciences
>> Software Product Management Widefield Research
>> Product Manager ­ Advanced Automated Analysis and Imaging Automation
>>
>>
>>
>> On Wed, 7 Jan 2015 07:31:13 +0000, Guiet Romain <[hidden email]>
>> wrote:
>>
>>> *****
>>> 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.
>>> *****
>>>
>>> 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 Š 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 doesn¹t 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 didn¹t find in ZEN any tool to swap channel / slice / time , as it is
>> possible to do in
>> ImageJ/Fiji.
>>
>> I hope it¹ll 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
>
> --
> ------------------------------------------------------------
> Steffen Dietzel, PD Dr. rer. nat
> Ludwig-Maximilians-Universität München
> Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
> Head of light microscopy
>
> Marchioninistr. 27
> D-81377 München
> Germany