Engineering at Oak-Tree

Links, articles, books, and resources

Resources

Articles and Insights

Understanding the big picture and how things fit together. Now, next, and beyond: trends in business, AI, and technology.

Lab Notes

Software development blog: sharing tools, techniques, concepts, and codes.

Code Server

Oak-Tree GitLab instance and code server

Tools and Libraries

Components, patterns, libraries, and architectures used for Oak-Tree projects.

Big Data Development

Oak-Tree Big Data development environment: Jupyter, MinIO, Kafka, and ZooKeeper.

Sonador

Sonador is an open source platform for AI powered applications which use medical imaging data.

Reference

Understanding DevOps

DevOps is an approach to developing, testing, and deploying software where the development team owns the entire lifecycle of the product.

Container Driven Development

Containers provide isolated, consistent, and portable software environments.

Microservice Architecture

Microservice architecture is a way of building systems where you separate components into small, separate projects that serve one purpose or functionality.

How To Build Python Packages

Python packages make your code available to the world. Here's how to create them.

What Is Data Science?

Revealing the insights within data that impacts our lives.

Models of Machine Learning

Data touches every aspect of our lives. Machine learning enables us to teach computers to understand and make use of the insight that they provide.

First Steps with PyTorch

PyTorch is a library that allows for deep learning models to be expressed in concise Python code. This article will introduce PyTorch and show how it can be used to consume pre-trained models for image classification.

Blockchain

Blockchain is hyped as one of the most transformative technologies in recent history. What is it? Why is it important? What kinds of problems can be solved using blockchain technologies?

Hyperledger Fabric

Hyperledger Fabric is becoming one of the most popular blockchain frameworks used by enterprises and medium-sized companies. What does it take to get started developing with it?

AI in Medical Imaging: Improving Diagnosis and Care

The promise of medical AI is a future where "the wisdom contained in the decisions made by nearly all clinicians and outcomes of billions of patients should inform the care of each patient." How do we get there?

What Is DICOM?

Overview of the DICOM standard and the role that it plays in the Sonador Data Platform.

Digital Imaging and Communications in Medicine

Technology standards used by healthcare organizations, biomedical device, and pharmaceutical companies for medical imaging and data management.

Detecting Lung Cancer with Artificial Intelligence (Part 1): Technical Challenges

Lung cancer is one of the world's most deadly and costly cancers. Early detection and treatment can reduce mortality rates and costs, but reliably spotting tumors in their early stages is a difficult challenge because such nodules are easy to overlook. AI systems for early detection could save millions of lives.

Detecting Lung Cancer with Artificial Intelligence (Part 2): Pathways to Solutions

Lung cancer remains the leading cause of death amongst cancers worldwide because it is difficult to detect. What impact would it have on patients, providers, and the healthcare system if it could be found and treated earlier?

Detecting Lung Cancer with Artificial Intelligence (Part 3): Sonador Lung AI

Sonador Lung AI is an initiative to create a solution for the early detection of lung cancer. It seeks to enable identification of lung nodules at an early stage, measure their progression to guide treatment, and provide integration with clinical systems to help manage care.

Sonador Medical Data Platform

Open-source cloud platform for medical imaging visualization and research. Project overview, technical aims, and links.

Quick Start

Be up and running with the Sonador Development environment in five minutes.

Documentation

Requirements, architecture, and technical reference for the Sonador project.

Examples and Tutorials

Jupyter notebooks and code samples showing how to work with data stored in Sonador.

IO: Architecture and Components

Sonador IO is the data management interface of Sonador used to securely store medical images so that they can be queried, retrieved, and transferred. It provides a streamlined way to share medical imaging data with other institutions across the Internet or other applications within the hospital.

AI: Architecture and Components

Sonador AI provides an end-to-end suite of tools and best practice guidance for Medical Imaging based machine learning. It includes a framework for implementing machine learning models on top of PyTorch, tools for creating annotated datasets, tracking experiments and model versions, deploying to production, and integrating AI into clinical workflows.

Security Overview

How are OpenID connect and oAuth2 used in Sonador to manage authentication of users and authorization of requests?

Processing Imaging Data with Sonador and Slicer

3D Slicer is a powerful tool which can be used to automate AI and other complex image processing tasks. This article provides an introduction to Slicer's scripting capabilities on Windows.

Modeling Data with NumPy: Images

NumPy is one of the fundamental packages used for data science, machine learning, and numerical computing within Python. This article provides an introduction to NumPy and how it is used for data modeling.

Modeling Data with NumPy: Tabulated/Structured Data

The simplest form of structured data encountered in many types of data analytics is that of "tabulated" or structured data. This article shows how NumPy can be used to ingest and inspect data from a structured text file.

Modeling Data with NumPy: Recognizing Hand-written Digits

Many machine learning questions include a sizable number of decisions about how you structure (or model) the data. In this article, we look at how to structure image data to classify handwritten digits using SciKit-Learn.

Modeling Data with NumPy: Image Volumes

In many types of medical imaging studies, such as CT and MRI, there is a sequence of stacked images acquired. These stacks can be ordered and worked with as a cohesive volume. In this article, we look at how to do so with NumPy in Python.