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

William Moore (Staff) W.Moore at dundee.ac.uk
Wed Aug 31 11:47:26 BST 2016

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,


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:


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 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
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