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Activities completed this month
The BMMR2: Breast Multiparametric MRI for prediction of NAC Response challenge has 3 submissions so far. MIDRC work is picking up as well as Microsoft work for kubernetes : MIDRC - we are getting azure credits to deploy MedICI with docker submissions. Should be this month (November) - Still hasn't happened (12.9.2021) I've been working to really make the image comparator code neat and organized. I want this project designed in a way that make additional features easy to add. I believe I've achieved that The addition of a new app that allows a unique pairwise classification has been added to the app for the MIDRC project specifically. This feature allows two images to be displayed by patient and the goal is to use this to figure out which studies by patient have both a lateral and frontal chest xray. It's a test for Challenge 0 (practice docker submission challenge). So basically this app will allows us to find studies with both a good frontal and lateral xray so that we can create a ground truth to give to challenge participants for Challenge 0. The goal is to have participants create an AI algorithm that can correctly identify frontal and lateral chest xrays. If this challenge goes well then more complex questions will be raised and a challenge built around those questions will be formulated. Image Added 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.

Activities completed this month

The BMMR2: Breast Multiparametric MRI for prediction of NAC Response challenge has 3 submissions so far.

MIDRC work is picking up

as well as Microsoft work for kubernetes

1. MIDRC - we are getting azure credits to deploy MedICI with docker submissions. Should be this month (November) - Still hasn't happened (12.9.2021)
2. I've been working to really make the image comparator code neat and organized. I want this project designed in a way that make additional features easy to add. I believe I've achieved that
3. The addition of a new app that allows a unique pairwise classification has been added to the app for the MIDRC project specifically. This feature allows two images to be displayed by patient and the goal is to use this to figure out which studies by patient have both a lateral and frontal chest xray. It's a test for Challenge 0 (practice docker submission challenge). So basically this app will allows us to find studies with both a good frontal and lateral xray so that we can create a ground truth to give to challenge participants for Challenge 0. The goal is to have participants create an AI algorithm that can correctly identify frontal and lateral chest xrays. If this challenge goes well then more complex questions will be raised and a challenge built around those questions will be formulated.
4. Image Added

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.

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 .Image Removed . - Still waiting on credits for Azure use.

Paused
Continue getting CodaLab running on NCI's network and VMs: Issues: 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. 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.

Paused

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.

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