[ENH] look into bioimage spec

[kaczmarj]

https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/model_spec_latest.md

Beware that this might not include microns resolution yet.

what we should probably do is be able to convert our configuration to this bioimage spec.

[kaczmarj]

see bioimage-io/bioimage.io#28 for minutes

and https://github.com/qupath/qupath-bioimageio-spec for parser in qupath

[oeway]

Hi @kaczmarj This is Wei from the BioImage Model Zoo, let us know if you need help in adopting our spec. You are also welcome to join our weekly meeting, and you can find the meeting time in the meeting minutes.

[kaczmarj]

thank you @oeway! is there any chance the BioImage spec will include the resolution at which deep neural networks are applied? for example, in digital pathology, the spacing is very important (often measured in micrometers per pixel). i did not see that option when i reviewed the spec.

[oeway]

Hi There was a discussion with Pete from the QuPath team, but we haven't incorporated into our spec yet, for now the option is to create your own custom under config, you can create your own key wsinfer and place any vendor specific spec inside, including spacing.

Here you can find an example.

We are considering refine the axes field to allow adding spacing etc., see here: bioimage-io/spec-bioimage-io#70

[kaczmarj]

that's great, thanks for the information.