Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Unit should be "micrometer" for compatbility with OME-NGFF #73

Open
krokicki opened this issue Mar 8, 2024 · 1 comment
Open

Unit should be "micrometer" for compatbility with OME-NGFF #73

krokicki opened this issue Mar 8, 2024 · 1 comment

Comments

@krokicki
Copy link

krokicki commented Mar 8, 2024

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
Copy link
Contributor

bogovicj commented Mar 8, 2024

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants