sanjeevani

Imaginea 2020 Inifnity Idea

Medical image processing and modeling:

• Segmentation
• Regression
• Classification
• Generation/Reconstruction
• Representation learning

Open Source Libraries

• https://niftynet.io/
• https://itk.org/
• https://vtk.org/
• https://www.kaggle.com/schlerp/getting-to-know-dicom-and-the-data/data

Papers

Format

• Dicom
• https://www.kaggle.com/schlerp/getting-to-know-dicom-and-the-data/data
• Nii
• http://paulbourke.net/dataformats/nii/

Datasets

• Realated to Lung

  • http://networkrepository.com/lung-cancer.php
  • https://archive.ics.uci.edu/ml/datasets/Lung+Cancer
  • https://lndb.grand-challenge.org/Home/
    • https://kits19.grand-challenge.org/data/
    • https://arxiv.org/pdf/1904.00445.pdf
  • http://biogps.org/dataset/tag/lung%20cancer/
  • https://www.cancerimagingarchive.net/ Needs to raise request for the dataset with a reason
    • https://wiki.cancerimagingarchive.net/display/Public/TCGA-LUAD 20GB
    • https://wiki.cancerimagingarchive.net/display/Public/ACRIN-FLT-Breast 70GB

• Breast Cancer

• https://wiki.cancerimagingarchive.net/display/Public/The+VICTRE+Trial%3A+Open-Source%2C+In-Silico+Clinical+Trial+For+Evaluating+Digital+Breast+Tomosynthesis 1TB

  • Download utils
  • https://github.com/DIDSR/VICTRE
  • https://github.com/DIDSR/VICTRE_DM_ROIs

• Eye

  • https://www.kaggle.com/paultimothymooney/kermany2018 5GB JPEG image classification
  • https://www.kaggle.com/benjaminwarner/resized-2015-2019-blindness-detection-images 17GB image classification Base dataset

• Chest

  • https://www.kaggle.com/c/rsna-pneumonia-detection-challenge 4GB Dicom possible 2nd dataset

Deep Learning

• Covulutional Network References

  • http://cs231n.stanford.edu/
  • http://cs231n.github.io/

• UNet

  • https://towardsdatascience.com/understanding-semantic-segmentation-with-unet-6be4f42d4b47
  • https://heartbeat.fritz.ai/deep-learning-for-image-segmentation-u-net-architecture-ff17f6e4c1cf

Papers

• Image PRocessing Pipelines:

• Nifty Pipeline PDF

  • https://niftynet.io/

• UNet

  • https://arxiv.org/abs/1505.04597
  • https://github.com/zhixuhao/unet

Pipeline Components

• Data loading

  • Load 3D images from different image formats
  • Anistropic voxels and special spatial information and patient information

• Data prepration as test/test/validation

• Image data loading and sampling

• Data augmentation

• DL Model Architecture

• DL framewok

• Metrics to evaluate

• Prediction

• https://towardsdatascience.com/object-oriented-machine-learning-pipeline-with-mlflow-for-pandas-and-koalas-dataframes-ef8517d39a12

Our choice of Tools

• AWS
  • S3
  • EMR
• Apache Spark
• MLFLOW
  • https://github.com/mlflow/mlflow/tree/master/examples/flower_classifier
• Tensorflow
• Kubernets (?)