Contribute to BioImage.IO

esgomezm commented 4 years ago

We have a model at Bioimage.io for which we want to upload a notebook. How could we do it? Should we include it in the manifest at our repository? How could I indicate "this model was the output of this notebook". Also, should I prepare a new yaml file for the notebook even if it is already created for the model?

oeway commented 4 years ago

We have a model at Bioimage.io for which we want to upload a notebook. How could we do it? Should we include it in the manifest at our repository?

Yes, since deepimagej is now a community partner, you can simply add the notebook to the manifest file at your repo. And you will need to create a notebook key, see examples in ZeroCostDL4Mic.

How could I indicate "this model was the output of this notebook"?

Assuming you have added the notebook to your yaml file, and assigned an id to it. You can then add a links field to the model description, and include the notebook id. Linking a notebook to a model is the same as linking an application (example).

Also, should I prepare a new yaml file for the notebook even if it is already created for the model?

No, you can simply fill the fields directly in your manifest.bioimage.io.yaml without creating another yaml file, just like the ZeroCostDL4Mic example.

esgomezm commented 4 years ago

Ok, done. I hope it works.

Assuming you have added the notebook to your yaml file, and assigned an id to it. You can then add a links field to the model description, and include the notebook id. Linking a notebook to a model is the same as linking an application (example).

If we want to add both, dataset and notebook, would we need just write one more line in links with dataset's id?

oeway commented 4 years ago

If we want to add both, dataset and notebook, would we need just write one more line in links with dataset's id?

Yes, exactly. I added more instructions here.

paxcalpt commented 4 years ago

Wei, I need to be able to cite more than an article in the yaml files. For example, stardist should have 2 citations from the original authors plus the ZeroCost citation for our modifications. How can I do this?

fjug commented 4 years ago

My two cents: One concrete model is either a 2D or a 3D stardist model, right? If the type of trained model is cited though, I agree, there wouldn’t be much space for citing training-related resources.

Currently the idea is to cite a description of the type of model. For example, we are also not citing Keras, Pytorch, etc. although we critically rely on it for virtually all models.

Still, this in not a particularly good answer and we will need to find a satisfactory solution. I just would like to avoid that the yaml files start looking like bibtex libraries... 😉

Best, Florian On 10. Jul 2020, 18:43 +0200, Ricardo Henriques notifications@github.com, wrote:

Wei, I need to be able to cite more than an article in the yaml files. For example, stardist should have 2 citations from the original authors plus the ZeroCost citation for our modifications. How can I do this? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

paxcalpt commented 4 years ago

Ok, this sounds reasonable. I'll then cite the Zero preprint which properly references the original sources for the networks

On Fri, Jul 10, 2020 at 5:50 PM Florian Jug notifications@github.com wrote:

My two cents: One concrete model is either a 2D or a 3D stardist model, right? If the type of trained model is cited though, I agree, there wouldn’t be much space for citing training-related resources.

Currently the idea is to cite a description of the type of model. For example, we are also not citing Keras, Pytorch, etc. although we critically rely on it for virtually all models.

Still, this in not a particularly good answer and we will need to find a satisfactory solution. I just would like to avoid that the yaml files start looking like bibtex libraries... 😉

Best, Florian On 10. Jul 2020, 18:43 +0200, Ricardo Henriques notifications@github.com, wrote:

Wei, I need to be able to cite more than an article in the yaml files. For example, stardist should have 2 citations from the original authors plus the ZeroCost citation for our modifications. How can I do this? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bioimage-io/bioimage-io-models/issues/26#issuecomment-656776220, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAF2O3NN4UIWPVK63CL6JLLR25BFZANCNFSM4OMMHXKQ .

-- Prof. Ricardo Henriques Research Group Leader at UCL Quantitative Imaging and Nanobiophysics group https://henriqueslab.github.io/

paxcalpt commented 4 years ago

Fixing this by adding a disclaimer in the ZeroCostDL4Mic notebook items "Note: visit the ZeroCostDL4Mic wiki to check the original publications this network is based on and make sure you cite these also."

On Fri, Jul 10, 2020 at 5:52 PM Ricardo Henriques paxcalpt@gmail.com wrote:

Ok, this sounds reasonable. I'll then cite the Zero preprint which properly references the original sources for the networks

On Fri, Jul 10, 2020 at 5:50 PM Florian Jug notifications@github.com wrote:

My two cents: One concrete model is either a 2D or a 3D stardist model, right? If the type of trained model is cited though, I agree, there wouldn’t be much space for citing training-related resources.

Currently the idea is to cite a description of the type of model. For example, we are also not citing Keras, Pytorch, etc. although we critically rely on it for virtually all models.

Still, this in not a particularly good answer and we will need to find a satisfactory solution. I just would like to avoid that the yaml files start looking like bibtex libraries... 😉

Best, Florian On 10. Jul 2020, 18:43 +0200, Ricardo Henriques notifications@github.com, wrote:

Wei, I need to be able to cite more than an article in the yaml files. For example, stardist should have 2 citations from the original authors plus the ZeroCost citation for our modifications. How can I do this? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bioimage-io/bioimage-io-models/issues/26#issuecomment-656776220, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAF2O3NN4UIWPVK63CL6JLLR25BFZANCNFSM4OMMHXKQ .

-- Prof. Ricardo Henriques Research Group Leader at UCL Quantitative Imaging and Nanobiophysics group https://henriqueslab.github.io/

-- Prof. Ricardo Henriques Research Group Leader at UCL Quantitative Imaging and Nanobiophysics group https://henriqueslab.github.io/

oeway commented 4 years ago

Wei, I need to be able to cite more than an article in the yaml files. For example, stardist should have 2 citations from the original authors plus the ZeroCost citation for our modifications. How can I do this?

@paxcalpt In fact, we support a list of citations, so you can just place a list of citations. see the example below:

    cite:
      - text: "Lucas von Chamier .... ZeroCostDL4Mic: an open platform to simplify access and use of Deep-Learning in Microscopy. bioRxiv, 2020."
        doi: https://doi.org/10.1101/2020.03.20.000133
      - text: "Ronneberger, Olaf et al. U-net: Convolutional networks for biomedical image segmentation. MICCAI 2015."
        doi: https://doi.org/10.1007/978-3-319-24574-4_28

wolny commented 3 years ago

Hi everyone, I'd like to submit 4 models to the Bioimage.io model zoo:

bioimage-io / bioimage-io-resources

Contribute to BioImage.IO #26