Need to populate list of ideas for GSoC 2019

[tvercaut]

I create a stub wiki page that now needs to be populated: https://github.com/NifTK/NiftyNet/wiki/Google-Summer-of-Code-(GSoC)-2019-Ideas-List

Feel free to use this issue to jot down rough ideas. We can then consolidate these on the wiki.

[tvercaut]

Random topics:

• Federated learning (e.g. https://github.com/tensorflow/privacy, https://github.com/OpenMined/PySyft)
• NiftyNet module API to integrate in larger software (see Embedding niftynet into a custom python code (a.k.a. module API) #124)
• Bridge tf.hub with the model zoo (see also Using pre-trained model in a way like TensorflowHub #254)
• video support
• NLP+images
• CUDA optimisation for resampling, CRF-as-RNN (see also Need an efficient 3D resampling op (e.g. trilinear resampler) #239)
• gradient checkpointing integration (see also Allow using gradient checkpointing #325 and https://github.com/openai/gradient-checkpointing)
• eager version of NiftyNet

[wyli]

• XNAT support (see also net_download should support XNAT #183 NiftyNet should be able to connect to an XNAT instance to fetch data #184)
• Fully automated Cross-validation hyper-parameter selection

[YipengHu]

• Links inference to OpenIGTLink, 3D Slicer, IGSTk and/or Plus Toolkit

[tvercaut]

@YipengHu: sounds great. This can be bundled with the video support. Would you be happy to act as a mentor if we get someone onboard? If so, would you mind writing a short project description for it on the wiki? Note the deadline for the full application (February 6, 2019 at 20:00 (GMT)).

[tvercaut]

@wyli If you are happy to act as a mentor in case we get a student, can you pick an idea you would be interested to mentor and write a short description for it on the wiki?

[YipengHu]

@YipengHu: sounds great. This can be bundled with the video support. Would you be happy to act as a mentor if we get someone onboard? If so, would you mind writing a short project description for it on the wiki? Note the deadline for the full application (February 6, 2019 at 20:00 (GMT)).

Definitely interested. I could not find any details for this though. Link to requirement for the project proposal?

[wyli]

@YipengHu: sounds great. This can be bundled with the video support. Would you be happy to act as a mentor if we get someone onboard? If so, would you mind writing a short project description for it on the wiki? Note the deadline for the full application (February 6, 2019 at 20:00 (GMT)).

Definitely interested. I could not find any details for this though. Link to requirement for the project proposal?

some guides here: https://google.github.io/gsocguides/mentor/defining-a-project-ideas-list

[tvercaut]

Brilliant. As far as I can see, there is no formal way for specific project proposals. You can look at a couple of examples coming from other organisation for last year's GSoC:

• https://github.com/CGAL/cgal/wiki/Project-Ideas
• https://github.com/osrf/osrf_wiki/wiki/GSoC18
• https://github.com/sympy/sympy/wiki/GSoC-2018-Ideas
• http://slam6d.sourceforge.net/wishlist.html

[tvercaut]

As discussed with @atbenmurray:

• Make NiftyNet's model zoo more accessible to user. Relevant pointers for this task:
  • Integrating with Slicer using DeepInfer: http://www.deepinfer.org
  • Cloud serving with TOMAAT https://github.com/faustomilletari/TOMAAT
  • Might be good to have a look at http://modelhub.ai
  • Would be great to make use of TF serving https://www.tensorflow.org/serving/

[tvercaut]

Would be nice to:

• Start the transition to the TF 2.0 API: https://www.tensorflow.org/versions/r2.0/api_docs/python/tf

[atbenmurray]

First attempt at writing a 'sales pitch' for the proposed activity
Making it easier to write new applications for the model zoo
Niftynet is a powerful deep learning suite for the medical imaging field; we want to build on its success so far making it even easier to develop cutting-edge models and deploy them to the Model Zoo. Niftynet provides you with a suite of tools that help you develop networks based on TensorFlow and give you pre- and post-processing functionality to help you integrate your network with medical imaging data sources and databases.
We intend to undergo a series of big improvements to the model building capability of Niftynet based on what we have learned from the model zoo thus far; our goal is to give model writers the means to create new applications with much less coding than before and to enable application writers to embed Niftynet networks into complex, interactive workflows.

[atbenmurray]

Also quite sales pitchy
Integrating Niftynet into Slicer
3D Slicer is a powerful open source tool for medical imaging informatics, image processing and 3D visualisation. It has a plugin architecture that allows integration of applications into Slicer and Slicer into applications, and our goal is to integrate Niftynet into Slicer so that Slicer can be used as the front end of a deep learning platform. Where possible, we'll leverage existing tools (such as deepinfer) to do some of the heavy lifting, so that we can focus on bringing Slicer users the capability to seamlessly train and validate models and visualise results without having to leave Slicer.

[tvercaut]

Thanks @atbenmurray, this looks good. Don't forget to update the wiki page today or tomorrow (i.e. before the deadline).

[atbenmurray]

Will do this ev Ben

…

On Mon, 4 Feb 2019, 17:09 Tom Vercauteren ***@***.*** wrote: Thanks @atbenmurray <https://github.com/atbenmurray>, this looks good. Don't forget to update the wiki page today or tomorrow (i.e. before the deadline). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#307 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AClN4YjoJztMi95mJ9jBxfUc_wpLx1xjks5vKFstgaJpZM4aD6ej> .

[atbenmurray]

If you mean this link https://github.com/NifTK/NiftyNet/wiki/Google-Summer-of-Code-(GSoC)-2019-Ideas-List I don't appear to have edit permissions.

…

On Mon, 4 Feb 2019 at 18:08, Ben Murray ***@***.***> wrote: Will do this ev Ben On Mon, 4 Feb 2019, 17:09 Tom Vercauteren ***@***.*** wrote: > Thanks @atbenmurray <https://github.com/atbenmurray>, this looks good. > Don't forget to update the wiki page today or tomorrow (i.e. before the > deadline). > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#307 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AClN4YjoJztMi95mJ9jBxfUc_wpLx1xjks5vKFstgaJpZM4aD6ej> > . >

[atbenmurray]

I currently don't have permission to edit the wiki. I'm off this week; happy to edit the wiki this evening or tomorrow evening, but if that is too late, then can you just add them in with Medium, benjamin murray at kcl.ac.uk?

[wyli]

adding you to the admin team @atbenmurray

[atbenmurray]

Done! Hopefully is in right format and good.

[tvercaut]

Unfortunately, our application to GSoC was not successful. I am thus closing this issue.