[ome-users] getPlanePositionZ for z-stage AND z-piezo from ND2 file

[William Moore (Staff)]

Hi Enno,

If you try opening your files in ImageJ/Fiji with the Bio-formats plugin and choose to
“Display Metadata” and “Display OME-XML metadata”, do you see anything there
that represents the z info you need?

 It would be really helpful if you could send us a sample ND2 file that has this metadata.
Then we can check if / where Bio-Formats is reading it.
Please let us know what values you’re expecting for the z-stage and z-piezo once you’ve
uploaded the file so we know what to look for.

You an upload files at https://www.openmicroscopy.org/qa2/qa/upload/

Many thanks,

  Will.



On 30 Aug 2016, at 12:00, Enno R. Oldewurtel <eoldewur at pasteur.fr<mailto:eoldewur at pasteur.fr>> wrote:

Dear all,

maybe someone can help me retrieving the metadata for z-positions from an ND2 file.
I have been using the following in the past:

m=r.pointer.getMetadataStore();
z=m.getPlanePositionZ(i,j).value;

But now I work on a Nikon microscope that has both a z-stage and a z-piezo. How can I retrieve the two z values? At the moment, getPlanePositionZ(i,j) gives me the position of the piezo.

Many thanks,
Enno


--
Enno Oldewurtel
Institut Pasteur
Laboratory of Microbial Morphogenesis and Growth
Bâtiment 26 François Jacob (2e étage)
28, rue du Docteur Roux
75724 Paris Cedex 15

eoldewur at pasteur.fr<mailto:eoldewur at pasteur.fr>
Office: +33 (0)1 45 68 86 12
https://research.pasteur.fr/en/team/microbial-morphogenesis-and-growth/
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20160831/eec38cb5/attachment.html>