Re: How to access OME Metadata?

Posted by Peterbauer Thomas on Aug 22, 2020; 7:52pm
URL: http://imagej.273.s1.nabble.com/How-to-access-OME-Metadata-tp5023870p5023871.html

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

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