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saalfeldlab / n5-ij

ImageJ convenience layer for N5
BSD 2-Clause "Simplified" License
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Unit should be "micrometer" for compatbility with OME-NGFF #73

Open krokicki opened 7 months ago

krokicki commented 7 months ago

When exporting with OME-NGFF metadata, the current plugin produces something like this:

{"path":"image/s0","axes":[{"type":"space","name":"x","unit":"micron"},{"type":"space","name":"y","unit":"micron"},{"type":"space","name":"z","unit":"micron"}],"coordinateTransformations":[{"scale":[0.2,0.13000001170000106,0.13000001170000106],"type":"scale"},{"translation":[0.0,0.0,0.0],"type":"translation"}]}

The unit "micron" is not recommended by the spec which instead recommends "micrometer". If this isn't possible, perhaps OME-NGFF can be petitioned to add "micron", since it is a common term and valid in UDUNITS-2.

bogovicj commented 7 months ago

good call.

The current behavior is that the plugin will take that from the metadata stored in the ImagePlus. Right now, users are free to put any string they want in there. Probably what it should to is "standardize" some known set of synonyms (um -> micrometers, microns -> micrometers, etc.).

In general though, I'd want to pass through whatever unit is there as is if we can't figure out how to standardize it.