How to access OME Metadata?

[Cammer, Michael-3]

Would you please help with how to access metadata imported with Bio-Formats for use in a macro?


We  have Zeiss CZI files with timing metadata that we need to access in ImageJ Fiji.


The metadata are opened using the Bio-Formats Import option "Display OME-XML metadata" and are placed in a text window that has a Java icon in the upper left.  Thsi window is not listed in any of the ImageJ menus.


Using a macro, we want to parse the metadata to extract the times for each plane.  However, we cannot figure out how to get the text data from this text window into the macro.  Doing this for the metadata in the other metadata window is easy, but help would be appreciated how to get the data from this XML window.


Best regards-


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


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[Peterbauer Thomas]

On 22.08.20 20:09, Cammer, Michael wrote:

> Would you please help with how to access metadata imported with Bio-Formats for use in a macro?
>
>
> We  have Zeiss CZI files with timing metadata that we need to access in ImageJ Fiji.
>
>
> The metadata are opened using the Bio-Formats Import option "Display OME-XML metadata" and are placed in a text window that has a Java icon in the upper left.  Thsi window is not listed in any of the ImageJ menus.
>
>
> Using a macro, we want to parse the metadata to extract the times for each plane.

A while ago, I've written an ImageJ plugin reading timestamps from Zeiss
(.czi), Olympus (.vsi), VisiView/Metamorph (.nd/.tif/.stk) and
Deltavision (.dv) files (these are formats used in our facility). You
can get it from the following page:

https://www.maxperutzlabs.ac.at/research/facilities/biooptics-light-microscopy

Scroll down to "Workstations, Servers, Software" and select the the
"Software" section.

Please take bugs for granted (image metadata are an infinite, malodorous
swamp) and, should you have a look into the source code, be lenient. The
VisiView/Metamorph parser is basically a collection of ugly and
inefficient workarounds for bugs in Bio-Format's Metamorph reader.
Likewise, all the rest could for sure be implemented in much better
ways. It has been tested with a very limited number of software versions
and files. It should run on Windows and Linux (I never tried MacOS) and
it should be macro-recordable (open the Macro Recorder while using it
via the dialog)

Best,

Thomas

--
---
Thomas Peterbauer
Central Facility BioOptics - Light Microscopy
Max Perutz Laboratories
Dr. Bohr-Gasse 9/3
A-1030 Vienna
[hidden email]
Phone [phone]
Mobile [phone]

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[CARL Philippe (LBP)]

Dear Michael,
You should be looking for the Bio-Formats Macro Extensions macros under the following link:
https://docs.openmicroscopy.org/bio-formats/5.8.2/users/imagej/index.html
and more particularly the following code:
https://github.com/ome/bioformats/blob/develop/components/bio-formats-plugins/utils/macros/planeTimings.txt
Have a nice end end of week-end,
Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : [phone]

----- Le 22 Aoû 20, à 20:09, Cammer, Michael [hidden email] a écrit :

Would you please help with how to access metadata imported with Bio-Formats for use in a macro?


We  have Zeiss CZI files with timing metadata that we need to access in ImageJ Fiji.


The metadata are opened using the Bio-Formats Import option "Display OME-XML metadata" and are placed in a text window that has a Java icon in the upper left.  Thsi window is not listed in any of the ImageJ menus.


Using a macro, we want to parse the metadata to extract the times for each plane.  However, we cannot figure out how to get the text data from this text window into the macro.  Doing this for the metadata in the other metadata window is easy, but help would be appreciated how to get the data from this XML window.


Best regards-


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


------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
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