X and Y coordinates based on pixels or metric values

Hi everyone,

I’m calculating distances between segmented cells based on the extracted X and Y coordinates. However, it’s unclear to me if the X and Y coordinates are pixel values or metric values? If they are pixel values, how can you determine the size of a pixel and if they are metric values, which unit is it?

Kind regards,
Toke

Dear @tcamps,

these are pixel values. If you have a RawDataFile rdf you can call
OrbitUtils.getImageScaleAndUnit(rdf)
to get the scale and unit.

If your image is an “official” format like NDPI you will get the unit in mu-meter, otherwise it will be pixels.

Regards,
Manuel

Thanks for your fast reply! I am using .czi files, is that also an ‘official’ format?

Kind regards,
Toke

sure, CZI is “officially” supported.
Manuel