Update (Empanada) 2D Instance Mitochondrial Segmentation in EM Images - 2D MitoNet

[bioimageiobot]

This is an automatic PR created by the @bioimageiobot regarding changes to the resource item 10.5281/zenodo.10391887.
The following version(s) will be added:

• 10396023 (version from 2023-12-16)

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• Passed the bioimage.io CI tests: static (and dynamic) validations
• The meta information for the RDF item is complete
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  • Naming is intuitive and descriptive, example: Multi-Organ Nucleus Segmentation (StarDist 2D)
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Maintainers: @abhishek-bhardwaj-IN

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Previous PRs of this resource: #696

[bioimageiobot]

preview

[abhishek-bhardwaj-IN]

@FynnBe I see this PR is merged, but the empanada model is still not available on bioimage.io website. Can you please help with this?

[FynnBe]

hi @abhishek-bhardwaj-IN
first of all thank you for this contribution to the model zoo and your patience!
As we are moving to a new backend I have uploaded your model to our new backend directly: https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/patient-owl/staged/1/files/bioimageio.yaml

[FynnBe]

the tests run atm here

[FynnBe]

unfortunately tests don't pass, I'll try to take a look at fixing the model soon.
In the meantime you can try to make the tests pass yourself using bioimageio.core==0.6.2

from bioimageio.core import test_description, save_bioimageio_package_as_folder

local = save_bioimageio_package_as_folder("patient-owl/staged/1", output_path="patient-owl-local")

summary = test_description(local)
summary.display()

Also I would highly recommend to avoid the model kwarg to Empanada2DInference. Why can these not be set after initialization via nn_module.load_state_dict()?

[abhishek-bhardwaj-IN]

@FynnBe Thanks for looking into it.
Right now its not possible to remove model from kwarg as that will require major refactoring, but it's on our list for upcoming release. Can we proceed as it is now? Also, I am attaching the empanada-bioimage zip file which passes the above test pipeline.

https://abhibhardwaj-my.sharepoint.com/:u:/g/personal/abhishek_abhibhardwaj_in/Ec05ARkUWv9PuZ2BlZCAE5ABojMixMs2WldiPX-pjWaUbQ?e=vrElpM

[FynnBe]

staged again: https://github.com/bioimage-io/collection/actions/runs/8986982672