Update Small Extracellular Vesicle TEM Segmentation (Fully Residual U-Net)

[bioimageiobot]

This is an automatic PR created by the @bioimageiobot regarding changes to the resource item 10.5281/zenodo.6559474.
The following version(s) will be added:

• 6559475 (version 1)

Please review the changes and make sure the new item or version(s) pass the following check list:

• Passed the BioImage.IO CI tests: static (and dynamic) validations
• The meta information for the RDF item is complete
  • The tags are complete and describe the model
  • Naming is intuitive and descriptive, example: Multi-Organ Nucleus Segmentation (StarDist 2D)
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  • Documentation is complete
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• Approved by at least one of the BioImage.IO admin team member.

Maintainers: @esgomezm

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[oeway]

@FynnBe Could you look into this one? We had at least one other PR has the same issue.

[FynnBe]

required tensorflow (version) is not available through conda...

Looking for: ['bioimageio.core', "tensorflow[version='>=1.12,<1.13']"]
  
  
  Encountered problems while solving:
    - package tensorflow-1.12.0-gpu_py27h956c076_0 requires tensorflow-base ==1.12.0 gpu_py27h8e0ae2d_0, but none of the providers can be installed
    

[FynnBe]

should we fetch tensorflow always with pip or just as a fallback?
@constantinpape what do you think?

edit: let's move this discussion to #469

[constantinpape]

@constantinpape what do you think?

Do what you think is right here, I currently don't have the bandwidth to deal with any of the day to day here.

(On a general note, we need to be aware that support for tf 1 is a huge technical debt...)

[FynnBe]

before #469 is resolves we can avoid this issue by providing a conda environment.yaml file that get's tensorflow with pip:

something like:

channels:
  - conda-forge
  - defaults
dependencies:
  - pip:
    - tensorflow=1.12

[FynnBe]

interestingly tf 1.12 is not available via pip either (anymore)

Could not find a version that satisfies the requirement tensorflow<1.13,>=1.12 (from versions: 1.13.1, 1.13.2, 1.14.0, 1.15.0, 1.15.2, 1.15.3, 1.15.4, 1.15.5, 2.0.0, 2.0.1, 2.0.2, 2.0.3, 2.0.4, 2.1.0, 2.1.1, 2.1.2, 2.1.3, 2.1.4, 2.2.0, 2.2.1, 2.2.2, 2.2.3, 2.3.0, 2.3.1, 2.3.2, 2.3.3, 2.3.4, 2.4.0, 2.4.1, 2.4.2, 2.4.3, 2.4.4, 2.5.0, 2.5.1, 2.5.2, 2.5.3, 2.6.0rc0, 2.6.0rc1, 2.6.0rc2, 2.6.0, 2.6.1, 2.6.2, 2.6.3, 2.6.4, 2.6.5, 2.7.0rc0, 2.7.0rc1, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.8.0rc0, 2.8.0rc1, 2.8.0, 2.8.1, 2.8.2, 2.8.3, 2.9.0rc0, 2.9.0rc1, 2.9.0rc2, 2.9.0, 2.9.1, 2.9.2, 2.10.0rc0, 2.10.0rc1, 2.10.0rc2, 2.10.0rc3, 2.10.0, 2.11.0rc0, 2.11.0rc1, 2.11.0rc2)

I suggest we use tf 1.13 if 1.12 is specified... will make another separate PR to change this. ... #504

[bioimageiobot]

preview
preview-collection-json

[esgomezm]

I think this version of the model is not updated. Can I close the PR and try uploading it again? Back in the time there was a problem with updating the rdf file

[FynnBe]

with protobuf pinned this model is ready to be merged!!
just checking with @esgomezm as this model has been pending for a while... any updates?
Otherwise go ahead and merge ;-)

[FynnBe]

I think this version of the model is not updated. Can I close the PR and try uploading it again? Back in the time there was a problem with updating the rdf file

there is no updated version yet on zenodo: https://zenodo.org/record/6559475#.Y2T_LHbMJjE

[esgomezm]

no sorry, there was another one in my zenodo account. I think it's because I tried to upload again to solve of the existing problems. I will merge this and let's see if there is no new PR coming :D