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bioimage-io / bioimage.io

Website for the BioImage Model zoo -- a model zoo for bioimage analysis.
https://bioimage.io
MIT License
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Quick review of all the models in the BioImage.io #308

Open carlosuc3m opened 1 year ago

carlosuc3m commented 1 year ago

Hello everyone, I am testing the download and run of every model in the BioImage.io model zoo for DeepIcy and I decided it would be interesting to document their state.

I have created the following (simple) spreadsheet with information about each model. I have colored orange what I thought that could be an issue (for example not being able to run on the BioEngine). I have also colored yellow if the model did not contain correct sample tifs for the Java softwares which has been briefly discussed with @constantinpape here.

For many of the highlighted problems in the document, I have already posted a comment on the model card. And for all the bioengine problems (marked as NOT WORK) I have already notified @oeway with a description of the issue. Another common problem, is that the zip file for DeepImageJ models is sometimes not up to date with the model shown in the model card.

Finally, my last concern, as mentioned in the document, is whether the models that only provide the pythorch weights could also provide the torchscript ones in order to be compatible with Java softwares and the bioengine. https://docs.google.com/spreadsheets/d/1qJV9KtbbSTm3AGMq8shPIoIt6n2U4L1LvmkqBWJz8Jw/edit?usp=sharing

Regards, Carlos

cc @esgomezm @lmoyasans @ivan-ea @FynnBe

oeway commented 1 year ago

Hi @carlosuc3m Thanks for the great initiative to make this list!

For the BioEngine, I noticed the models are not synchronized to the server, and I have just did it manually, you should get more models available now. Note that we also skip some models because they don't provide any of the supported weights format. You can see the list here: https://github.com/bioimage-io/bioengine-model-runner/blob/gh-pages/manifest.bioengine.yaml

carlosuc3m commented 1 year ago

Hi @oeway

For the BioEngine, I noticed the models are not synchronized to the server, and I have just did it manually, you should get more models available now

Great I will check the models again and update the list

Note that we also skip some models because they don't provide any of the supported weights format. You can see the list here: https://github.com/bioimage-io/bioengine-model-runner/blob/gh-pages/manifest.bioengine.yaml

I know, but I thought it would be good to keep that in mind.

By the way, feel free to add any field or anotate anything on the list

carlosuc3m commented 1 year ago

https://github.com/bioimage-io/bioengine-model-runner/blob/gh-pages/manifest.bioengine.yaml in this file the models supported by the BioEngine are listed (as per @oeway )