SUMMARY.md

Table of contents

• Welcome!
• 🚀 Getting started
• Core functions
• Frequently asked questions
• Support
• Key pointers
• Publications
• IDC team
• Acknowledgments

Introduction

• Features
• Google Cloud Platform (GCP)
  • Getting started with GCP
• Amazon AWS platform
• DICOM
• Requesting GCP cloud credits
• Requesting AWS cloud credits

Tutorials

• Python notebook tutorials
• Slide microscopy
  • Using QuPath for visualization

Data

• Introduction
• Data versioning
• Organization of data
  • Files and metadata
  • Resolving CRDC Globally Unique Identifiers (GUIDs)
  • Clinical data
  • Organization of data, v2 through V13 (deprecated)
    • Files and metadata
    • Resolving CRDC Globally Unique Identifiers (GUIDs)
    • Clinical data
  • Organization of data in v1 (deprecated)
• Downloading data
  • Downloading data with s5cmd
• Data release notes
• Data known issues

DICOM

• Introduction to DICOM
• Data model
• Original objects
• Derived objects
  • DICOM Segmentations
  • DICOM Radiotherapy Structure Sets
  • DICOM Structured Reports
• Coding schemes
• DICOM-TIFF dual personality files
• IDC DICOM white papers

Portal

• Getting started
• Exploring data and cohorts
  • Exploring imaging data
  • Viewing collections, studies, and series
  • Understanding cohorts
• Cohort manifests
• Visualizing images
• Proxy policy
• Viewer release notes
• Portal release notes
• Portal known issues

API

• Getting Started
• IDC API Concepts
• Manifests
• Accessing the API
• Endpoint Details
• V1 API
  • Getting Started
  • IDC Data Model Concepts
  • Accessing the API
  • Endpoint Details
  • Release Notes

Cookbook

• Colab notebooks
• BigQuery
• Data Studio
  • Dashboard for your cohort
  • More dashboard examples
• ACCESS allocations
• Compute engine
  • 3D Slicer desktop VM
  • Using a BQ Manifest to Load DICOM Files onto a VM
  • Using VS Code with GCP VMs
  • Security considerations
• NCI Cloud Resources