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hpa_image_analysis's Introduction

HPA image-distance study on malignant transformation

Setup

  1. configure credentials

    Create file config.py in repo top-level containing a dictionary config that contains mongo, s3, and nferx credentials

  2. start docker environment

    prerequisites:

    • docker
    • nvidia-docker
    cd docker && make bash

Components

  • utils: modules
  • notebooks: experiments
  • docker: image processing compute environment

See also

design doc

hpa_image_analysis's People

Contributors

mbadge avatar martinkang93 avatar

Watchers

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hpa_image_analysis's Issues

embedding views

Martin has already generated embedding views for TSNE colored by HPA metadata.

We'd now like to overlay Dr. Lo's new labels onto the prior TSNE data.

🐛 only a subset of data was used for TSNE for computational simplicity, and most of Dr. Lo's images are not in this subset

🛣️ ⚖️

  • proceed with <10 joint samples
  • use PCA so that all data can be rotated
  • resubsample and compute TSNE so that all of Dr. Lo's samples are included

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