Allow direct search and download from BioImage Model Zoo
Opened this issue · 7 comments
Hey @oeway are you coming to EMBL on 11 March? I'll pass by and consult you the best way of allowing users to use models from Zoo in PlantSeg.
Unfortunately I won't be able to join, however Weize @Nanguage will join, so please discuss with him.
Not sure what you mean exactly, but maybe you can create a bioengine app for plantseg, basically a tailored version of https://github.com/bioimage-io/bioengine-web-client
Hi qin-yu, I will participate in the Hackathon. We can communicate face-to-face then!
Current PlantSeg model zoo
PlantSeg has a YAML file with hard-coded records of models including the link to weight files on Zenodo.
Adding BioImage.IO model zoo: Method 1
Since all models from PlantSeg are uploaded to BioImage.IO and Zenodo, we can simply update the list of models in the PlantSeg model zoo at start-up.
- Discover all compatible models
- Avoid duplicate in the local record (by removing current hard-coded record completely?)
- Separate the dropdown list by a horizontal line and ideally a section name
Adding BioImage.IO model zoo: Method 2
To minimise the changes, add a widget to let users add a model from BioImage.IO model zoo just like adding a custom model.
- Discover all compatible models
- Show models in that widget for users to add
Adding BioImage.IO model zoo: Method 3
Why bother running inference on our own code and filter BioImage.IO model zoo? Just use bioimageio.core and use all models available on the zoo : )
My Plan
Maybe I don't have to directly change the core of PlantSeg inference to bioimageio.core.
- Add compatible BioImage.IO model zoo records in PlantSeg on startup
- Replace PlantSeg hard-coded records by 1
- Add bioimageio.core as alternative inference engine
- Replace PlantSeg inference by 3
Potential Issues
- If PlantSeg wants to go generic in bioimage community, using bioimageio.core would greatly benefit PlantSeg; otherwise, PlantSeg loses the generalist capability of growing into segment-everything tool