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get physical z size of czi image

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

get physical z size of czi image

Postby pospiech » Thu Jul 02, 2015 10:17 am

I am using latest bioformats matlab implementation.
I can print out all >10000 elements of the metadata, but so far could not find the entry for the physical z resolution of an image. The image is a x-z plane of a zstack. I am interested in both the x and z (in the image y) pixel size in µm.
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Re: get physical z size of czi image

Postby sbesson » Thu Jul 02, 2015 12:14 pm

Hi,

If existing, the pixel size should be stored in the OME-XML metadata object populated when the file reader is initialized. It can be retrieved using the `getPixelsPhysicalSize[XYZ]` method. See this section for an example using Bio-Formats and MATLAB.

Best,
Sebastien
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