reading and modifying meta information from a czi

[Mikel Ariz Galilea]

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

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[ctrueden]

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
>

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

[Mikel Ariz Galilea]

Hi Curtis,

Thank you for the clarification, it's going to be helpful. I will check the
examples and decide what suits our needs best.

Thanks again.
Regards,

Mikel

2015-09-29 16:40 GMT+02:00 Curtis Rueden <[hidden email]>:

> 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
>

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