NIH | National Cancer Institute | NCI Wiki  

Error rendering macro 'rw-search'

null

Versions Compared

Old Version 2

changes.mady.by.user Unknown User (bearceba)

Saved on

compared with

New Version 3

changes.mady.by.user Unknown User (bearceba)

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Activities completed this month
  1. I finished re-writing the transcript for Carolyn.
  2. Reminded Jayashree to send invoices for Sept (new contract).
  3. Finished UI development and api construction of docker image upload.
  4. Received scoring program for SPIE-AAPM Breast Cancer Challenge. Added to challenge site.
  5. Updated SPIE-AAPM site to include new validation phase data.
  6. Get PIV card for NIH access (appointment is scheduled for 12/22/2020). UPDATE: Done
  7. Kevin Olexa, from NCI is tried upgrading the JQuery of their deployment of the codalab MedICI instance over at NCI/NIH. It seems it will be a lot of work. The new plan is to have me try out the v2 codalab otherwise known as codabench (https://www.codabench.org/). This was built with python3 and jQuery 3+. This should circumvent any issues with up to date packages.
Planned for next month
  1. The SPIE-AAPM Breast Cancer challenge has started (25 participants). Challenge link: http://spie-aapm-nci-dair.westus2.cloudapp.azure.com/. Will need to double check that they have the scoring program ready (I know it is not right now..).
  2. Updated SPIE-AAPM site to include new validation phase data.
  3. Add support link and message regarding using the api for image and metadata downloads.
  4. Investigated Kheops and am finishing the report.
Planned for next month
  1. Add Okta as supported feature in MedICI GitHub and website.
  2. Wrap up the SPIE-AAPM Breast Challenge and collect final scores for the challenge organizers. 
  3. Continue ascertaining the validity of v2 codalab (codabench)
  4. Add support link and message regarding using the api for image and metadata downloads.
  6. Finish creating the MedNIST sample challenge on COVID-Kubernetes deployment and address some bugs listed below:
    1. In results table the "FILENAME" is always "trackingid", needs to be the image that was submitted.
    2. Image Uploads are slow and we need to address that. 
    3. Sometimes deleting an image from the repo changes the image upload html and I have to reset it. This shouldn't happen.
  7. Setup DL-sparse-view CT Grand Challenge (I'm a little behind on this)
Comments

Things that went well:

SPIE-AAPM Challenge for reference:

http://spie-aapm-nci-dair.westus2.cloudapp.azure.com/


  • I have Patrick's code loaded and working almost in the cloud. While extremely close, the COVID challenge this was being built for will need to proceed with plan b. This is the standard docker submission we have talked about and will also have Okta integration and docker upload functionality. We won't need to go with plan-b anymore as it seems the kubernetes cluster deployment is working well.
  • Scoring program integration for SPIE-AAPM was seamless. Mateusz Buda, a data scientist working on the Breast challenge, created an easy to use evaluation script that I could tie into codalab and is being used to score submissions.
  • I have the start of the codabench deployed and it almost works. There is a problem with the static files not being able to be found so there is no style on the web app when browsed to.
  • The forum and issue tracker were used in the SPIE-AAPM challenge



Things that could be improved:

  • SPIE challenge test phase leader board was showing multiple submissions by participants and should only show their best score. I can and did fix it manually but it's not ideal.
MeetingDate
Bi-weekly Meeting #1

 

Bi-weekly Meeting #2

...