Re: reading and modifying meta information from a czi

Posted by ctrueden on Sep 29, 2015; 2:40pm
URL: http://imagej.273.s1.nabble.com/reading-and-modifying-meta-information-from-a-czi-tp5014488p5014491.html

Hi Mikel,

> I need to read the meta information contained in a CZI file, and I
> would like to manually edit some of the fields and save the file
> again.

ImageJ cannot do this. The Bio-Formats library reads and converts
proprietary file formats (PFFs) like CZI into standard formats like
OME-TIFF. It does not, and will not in the future, save data to those
PFFs—especially the more complex ones like CZI.

See this article for details:
* http://jcb.rupress.org/content/189/5/777.full

What you can do is read out the metadata from your CZI, modify it, and then
save the result to a standard open format—most likely OME-TIFF.

You can find some examples of how to call Bio-Formats from Java code at:
*
http://www.openmicroscopy.org/site/support/bio-formats5.1/developers/java-library.html

The PrintTimestamps example shows how to read metadata as OME-XML:
*
https://github.com/openmicroscopy/bioformats/blob/v5.1.4/components/formats-gpl/utils/PrintTimestamps.java

And MinimumWriter shows how to write out an image file:
*
https://github.com/openmicroscopy/bioformats/blob/v5.1.4/components/formats-gpl/utils/MinimumWriter.java

Or you could just write out the OME-XML string to a .ome.xml file,
depending on your needs.

Further questions about how to use Bio-Formats can be directed to the OME
team; see:
* http://www.openmicroscopy.org/site/community

Regards,
Curtis

On Tue, Sep 29, 2015 at 6:22 AM, Mikel Ariz Galilea <[hidden email]>
wrote:

> Hi all,
>
> I need to read the meta information contained in a CZI file, and I would
> like to manually edit some of the fields and save the file again.
> Specifically, I am trying to modifiy the (X,Y) positions of the microscope
> for the different scenes stored. Is that possible?
> I have read about the ZeissCZIReader (
>
> http://www.openmicroscopy.org/site/support/bio-formats5.1/formats/zeiss-czi.html
> )
> but I am not sure on how to use it for this purpose.
>
> Thanks in advance for any hint or suggestion.
>
> Mikel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html