README.md

A collection of resources for Healthcare. In case something is missing or a link is not working, please create an issue here

Communities

• RSNA: Radiological Society of North America
  • RSNA MIRC Medical Imaging Resource Center (MIRC) project overview
  • RSNA MIRC CTP Describes the RSNA MIRC Clinical Trials Processor (CTP), a stand-alone image processing application for imaging clinical trials data.
  • RSNA Practice Tools
• ASTRO: American Society for Radiation Oncology

DICOM - Digital Imaging and Communications in Medicine

• Wikipedia DICOM
• DICOM Standard Browser Documentation of all DICOM headers accompanied by a DICOM headers viewer.
• DICOM is easy blog A blog on DICOM file format to get you started.
  • Getting oriented using image plane module Understand 3D images stored on DICOM and their orientation.
• dcm2niix A command line (terminal) utility to convert files from DICOM to NIFTI format.
  • dcm2niix: Gantry tilt error Understand dcm2niix error outputs.

NIFTI - Neuroimaging Informatics Technology Initiative

• Wikipedia: NIFTI
• NIFTI Format
  • NIFTI-1 explained
  • NIFTI-2 explained

Medical images View & Processing

• Coordination System: Images orientation can vary from file to file and it is important then to have a consistent orientation when processing them especially in batches.
  • Coordinate systems explained I
  • Coordinate systems explained II
• Understanding window width and window center Window width and center affect what you see in an image.
• SimpleITK: Open-source multi-dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++
  • Read DICOM series from array
  • SimpleITK does not save metadata Metadata issues with SimpleITK
• Viewers
  • ITK-snap: View and process NIFTI files.
    • ITK-snap beginners short tutorial
  • Paraview An STL File viewer of 3D rendered objects.
  • VTK: Process images and create 3D computer graphics with the Visualization Toolkit
    • PyScience - VTK
    • A Comprehensive Guide To Visualizing and Analyzing DICOM Images in Python
  • Python Matplotlib
    • Viewing 3D Volumetric Data With Matplotlib
• Burnt-in Images Text
  • Tesseract: Optical Character Recognition (OCR)
    • Frequently Asked Questions
    • [Tesseract User Manual[(https://tesseract-ocr.github.io/tessdoc/Home.html)
    • Tesseract OCR: Understanding the Contents of Documents, Beyond Their Text
    • How to OCR with Tesseract, OpenCV and Python
    • Text Extraction from a Table Image, using PyTesseract and OpenCV
    • Improving the quality of the output
    • A list of useful control parameters and config files
    • Using Config Files
    • Command Line Usage
  • PyTesseract Tesseract implementation in Python
    • Tesseract Page Segmentation Modes (PSMs) Explained: How to Improve Your OCR Accuracy
    • Language Translation and OCR with Tesseract and Python
    • Whitelisting and Blacklisting Characters with Tesseract and Python

Commercial and non-commercial de-identfication and anonymization tools

• Carina AI DeIdentifier The de-identifier I implemented from scratch including the algorithms and the user interface and is used by major healthcare players.
• AWS De-identification
• Google De-identification
• Free imaging software for anonymization

Spatial Patterns Analysis

• UPenn Notebook on spatial data analysis Useful for examining (cellular) populations interactions and other applications.
• Testing for inhomogeneity of spatial data