cannot get timestamps with new Zeiss 700

[mcammer]

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For years we have been using the Zeiss 710 for timelapse experiments.  When we open the files using the BioFormats importer in ImageJ the metadata reports a start time for the experiments and timestamps for each timepoint.

Last night I did a timelapse experiment with a new Zeiss 700 and when I opened the files there were no metadata for the experiment time nor timestamps.  There is, however, a tag that says
Information|Image|T|BinaryList|AttachmentName| #1               TimeStamps

Does anyone know how we can get the start time and timestamps info?  We need both.

Thank you!

===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/

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[mcammer]

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I overlooked that the files from the Zeiss 710 have a .lsm extension and files from the 700 have a .czi extension.  So Zeiss changed the file format.

If anyone knows how we can get the timing information out of the .czi format it would be greatly appreciated.

Thank you!

===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael
Sent: Wednesday, June 25, 2014 10:05 AM
To: [hidden email]
Subject: cannot get timestamps with new Zeiss 700

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For years we have been using the Zeiss 710 for timelapse experiments.  When we open the files using the BioFormats importer in ImageJ the metadata reports a start time for the experiments and timestamps for each timepoint.

Last night I did a timelapse experiment with a new Zeiss 700 and when I opened the files there were no metadata for the experiment time nor timestamps.  There is, however, a tag that says
Information|Image|T|BinaryList|AttachmentName| #1               TimeStamps

Does anyone know how we can get the start time and timestamps info?  We need both.

Thank you!

===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/

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[Niko Ehrenfeuchter]

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Dear Michael,


> I overlooked that the files from the Zeiss 710 have a .lsm extension and files from the 700 have a .czi extension.  So Zeiss changed the file format.

this depends on the version of the Zeiss software you're using, iirc.


> If anyone knows how we can get the timing information out of the .czi format it would be greatly appreciated.

Have you tried with the latest version of BioFormats, e.g. by a fresh
copy of Fiji? There were a lot of changes and bug fixes recently done by
the developers...

Cheers
~Niko


--
Niko Ehrenfeuchter
Imaging Core Facility
Kragenbau, Room G1055
Biozentrum, University of Basel
Klingelbergstrasse 50/70
CH-4056 Basel (Switzerland)

Office:  [phone]
Email:   [hidden email]

[Michael Schell-2]

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I can open a .czi file using the Bioformats importer packaged in Fiji.  If you check the “show metadata” box, you can see the timestamp info.

Michael

On Jun 25, 2014, at 11:16 AM, Niko Ehrenfeuchter <[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.
> *****
>
> Dear Michael,
>
>
>> I overlooked that the files from the Zeiss 710 have a .lsm extension and files from the 700 have a .czi extension.  So Zeiss changed the file format.
>
> this depends on the version of the Zeiss software you're using, iirc.
>
>
>> If anyone knows how we can get the timing information out of the .czi format it would be greatly appreciated.
>
> Have you tried with the latest version of BioFormats, e.g. by a fresh copy of Fiji? There were a lot of changes and bug fixes recently done by the developers...
>
> Cheers
> ~Niko
>
>
> --
> Niko Ehrenfeuchter
> Imaging Core Facility
> Kragenbau, Room G1055
> Biozentrum, University of Basel
> Klingelbergstrasse 50/70
> CH-4056 Basel (Switzerland)
>
> Office:  [phone]
> Email:   [hidden email]

[Douglas Richardson]

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You can also just save the files on the 700 as .lsm instead of the .czi
default

-Doug


On Wed, Jun 25, 2014 at 11:21 AM, Michael Schell <[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.
> *****
>
> I can open a .czi file using the Bioformats importer packaged in Fiji.  If
> you check the “show metadata” box, you can see the timestamp info.
>
> Michael
>
> On Jun 25, 2014, at 11:16 AM, Niko Ehrenfeuchter <
> [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.
> > *****
> >
> > Dear Michael,
> >
> >
> >> I overlooked that the files from the Zeiss 710 have a .lsm extension
> and files from the 700 have a .czi extension.  So Zeiss changed the file
> format.
> >
> > this depends on the version of the Zeiss software you're using, iirc.
> >
> >
> >> If anyone knows how we can get the timing information out of the .czi
> format it would be greatly appreciated.
> >
> > Have you tried with the latest version of BioFormats, e.g. by a fresh
> copy of Fiji? There were a lot of changes and bug fixes recently done by
> the developers...
> >
> > Cheers
> > ~Niko
> >
> >
> > --
> > Niko Ehrenfeuchter
> > Imaging Core Facility
> > Kragenbau, Room G1055
> > Biozentrum, University of Basel
> > Klingelbergstrasse 50/70
> > CH-4056 Basel (Switzerland)
> >
> > Office:  [phone]
> > Email:   [hidden email]
>

[mcammer]

Thanks for the replies both on & off list.

The simplest way to solve this problem is to use Save As and choose the LSM format since this works fine with the LOCI plugins for importing into ImageJ.

Regards,
Michael

===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/



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