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Activities completed this month

  • MIDRC work is picking up:
      1. I've made may small changes including:

        1. keyboard shortcuts for selecting images with arrow keys:
        2. Reject modal for discussing what's wrong with an image pair if there is an issue.
  • DAIR Digital Breast Tomosynthesis Cancer Detection Challenge - Phase 2 (DBTex2) - Dr. Mateusz Buda has reached out about a potential data problem for the test phase. I have send the code and data I used and we are working to make sure the challenge results from participants are accurate.Will be in touch with him over the next couple days to make sure everything is in order. 
  • Tested new github commits to the codalab framework code. They have merged in code that was porting the proiect to python3 (previously I was doing this on my own). It still has some issues. Will keep monitoring it so we can get an updated codalab base for our projects.
Planned for next month
  • MIDRC Challenge 0 which will feature docker submissions as well as the Image Comparator app and a jupyter notebook for annotator analysis. - Still waiting on credits for Azure use.
  • Jayashree has me collaborating with Steve Piper (sponsored collaborator) who has built a way to make OHIF (medical imaging viewer) talk to a database called couchdb. This is a nosql record style database that the app I'm buillding for MIDRC is based on. The plan is to integrate OHIF into this app and be able to launch beside codalab and MedICI in general. This would allow ePAD and caMicroscope like functionality with more flexibility as well. Progress on this will come soon as I dive in.
  • Figure out how to add a phase to a challenge (SPIE specifically with Dr. Mazurowski but maybe others as well).
  • Resecure DL Sparse certificate
Paused
  1. Continue getting CodaLab running on NCI's network and VMs:
    1. Issues:
      1. Credentials for AWS bucket not active and we cannot talk to the bucket. Need to reach out to Tony Bigham (tony.bigham@nih.gov) to get those refreshed. 
      2. On my local machine I deployed the updated CodaLab code and tried connecting to my own S3 bucket instance. I noticed that there is a javascript error making the request to the bucket. I need to setup up a similar but more simple setup to figure out how to upload data to s3 via javascript http requests so that I can trouble shoot the error on NCI's system and or mine. If we could use Azure, this might be resolved.

MeetingDate
Bi-weekly Meeting #1

 

Bi-weekly Meeting #2


Milestones

DescriptionDate
MIDRC app complete and allows for flexible annotation of images for ground truth generation

 



Task in Progress

DescriptionStatusCreation DateClose Date
  • Troubleshooting a javascript http request to Amazon AWS S3 bucket (paused for a bit)
Paused

 


Risks

Description

Mitigation

Rank

Status

Creation Date

Realization

Close Date

Continuous development of CodaLab on NCI's network is exposing bugs in deployment and or CodaLab itself. This isn't an issue in theory, but I don't know how many issues I'll need to correct in order for the system to work. It is hard to estimate time to completion as a consequence.Kevin Olexa and I are working together to address each as they come up. 1In Progress

 





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