Zeiss 880 timing question

[Cammer, Michael-2]

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We have been trying to do FRAP experiments on the Zeiss 880, but we are having difficulties getting accurate times.


Typically, we take 2 to 4 before images, then a bleach, and then the recovery sequence.


The problem is that we do not know how to get accurate times for the sequence after the bleaching.  I used to do this on a Leica SP2 and the times were well reported in the metadata, but I cannot find the times in the Zeiss files.  Any help would be appreciated.


Thank you.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

[hidden email]<mailto:[hidden email]>  http://nyulmc.org/micros  http://microscopynotes.com/

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[Uzi Hadad]

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Did you tried to look at the table in Mean ROI tab? I'm pretty sure you can
get it there.

Uzi

Uzi Hadad, PhD
Shared Resource Laboratory for Flow Cytometry & Bio-Imaging
Ilse Katz Institute for Nanoscale Science and Technology
Ben-Gurion University of the Negev
Beer Sheva 84105, Israel
Office: [phone] | Blgd 51, Room 325
Lab: [phone] | Room 326

On Wed, Aug 19, 2020, 23:44 Cammer, Michael <
[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.
> *****
>
> We have been trying to do FRAP experiments on the Zeiss 880, but we are
> having difficulties getting accurate times.
>
>
> Typically, we take 2 to 4 before images, then a bleach, and then the
> recovery sequence.
>
>
> The problem is that we do not know how to get accurate times for the
> sequence after the bleaching.  I used to do this on a Leica SP2 and the
> times were well reported in the metadata, but I cannot find the times in
> the Zeiss files.  Any help would be appreciated.
>
>
> Thank you.
>
>
> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
>
> NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY
> 10016
>
> [hidden email]<mailto:[hidden email]>
> http://nyulmc.org/micros  http://microscopynotes.com/
>
> Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567
>

[Rebecca M. Williams]

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Hi Michael --

As I recall this info is remarkably difficult to get.  The only way I could get it was to have zen display a timepoint on the images.  You do this using the graphics tab under the display.  Make sure you have "show all" checked (hidden to the right).  Choose the More. . . option and then coordinate -> time.

Becky


Rebecca Williams
Director, BRC Imaging Facility
B35 Weill Hall
Cornell University
[phone]



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael
Sent: Wednesday, August 19, 2020 4:44 PM
To: [hidden email]
Subject: Zeiss 880 timing question

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We have been trying to do FRAP experiments on the Zeiss 880, but we are having difficulties getting accurate times.


Typically, we take 2 to 4 before images, then a bleach, and then the recovery sequence.


The problem is that we do not know how to get accurate times for the sequence after the bleaching.  I used to do this on a Leica SP2 and the times were well reported in the metadata, but I cannot find the times in the Zeiss files.  Any help would be appreciated.


Thank you.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

[hidden email]<mailto:[hidden email]>  http://nyulmc.org/micros  http://microscopynotes.com/

Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567

[Toth, Peter Tibor]

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Hi Michael,

You can drop the Zeiss .czi file into Fiji. In the Metadata viewing column check the "Display OME-XML metadata" checkbox.  Metadata with times, etc.  opens up in a separate window.

-Peter






--

Peter T. Toth, PhD

Director, Fluorescence Imaging Core

The University of Illinois at Chicago

835 S. Wolcott Ave (MSB), E-325

Phone: [phone]

[hidden email]

________________________________
From: Confocal Microscopy List <[hidden email]> on behalf of Cammer, Michael <[hidden email]>
Sent: Wednesday, August 19, 2020 3:43 PM
To: [hidden email] <[hidden email]>
Subject: Zeiss 880 timing question

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We have been trying to do FRAP experiments on the Zeiss 880, but we are having difficulties getting accurate times.


Typically, we take 2 to 4 before images, then a bleach, and then the recovery sequence.


The problem is that we do not know how to get accurate times for the sequence after the bleaching.  I used to do this on a Leica SP2 and the times were well reported in the metadata, but I cannot find the times in the Zeiss files.  Any help would be appreciated.


Thank you.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

[hidden email]<mailto:[hidden email]>  http://nyulmc.org/micros  http://microscopynotes.com/

Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567

[Cammer, Michael-2]

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I want to thank the many replies to my question including from Zeiss directly.

I had been struggling with the regular metadata and didn't even think to look at the XML version separately.  

This may also answer a question someone asked about FRAP a few weeks ago.  In addition to the Elyra images, I opened a FRAP sequence from the Zeiss 880 and while not all the information to reconstruct the settings is displayed, this combined with the ROIs may be sufficient to run the analyses.

Best regards-

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
Office: 646-501-0567 Cell: 914-309-3270  [hidden email]  
http://nyulmc.org/micros  http://microscopynotes.com/
 



-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Toth, Peter Tibor
Sent: Thursday, August 20, 2020 12:35 PM
To: [hidden email]
Subject: Re: Zeiss 880 timing question

[EXTERNAL]

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Hi Michael,

You can drop the Zeiss .czi file into Fiji. In the Metadata viewing column check the "Display OME-XML metadata" checkbox.  Metadata with times, etc.  opens up in a separate window.

-Peter






--

Peter T. Toth, PhD

Director, Fluorescence Imaging Core

The University of Illinois at Chicago

835 S. Wolcott Ave (MSB), E-325

Phone: [phone]

[hidden email]

________________________________
From: Confocal Microscopy List <[hidden email]> on behalf of Cammer, Michael <[hidden email]>
Sent: Wednesday, August 19, 2020 3:43 PM
To: [hidden email] <[hidden email]>
Subject: Zeiss 880 timing question

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We have been trying to do FRAP experiments on the Zeiss 880, but we are having difficulties getting accurate times.


Typically, we take 2 to 4 before images, then a bleach, and then the recovery sequence.


The problem is that we do not know how to get accurate times for the sequence after the bleaching.  I used to do this on a Leica SP2 and the times were well reported in the metadata, but I cannot find the times in the Zeiss files.  Any help would be appreciated.


Thank you.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

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