Medical Imaging

63 minutes to read

In the majority of medical institutions, all images are stored in the so-called PACS. PACS (Picture Archiving and Communication System) is a technology used to store and transmit digital images and medical reports securely and reliably. The system overview: Picture Archiving and Communication System.

To speak with the doctors in the same language it’s highly recommended to get familiar with the basics of anatomy and corresponding terminology:

• General anatomy and radiographic positioning terminology

• Anatomical position

DICOM

13 minutes to read

Most of the time, you can find medical images stored in the DICOM files. This format is useful because it allows medical institutions to store (and transmit using DICOM standard) sensitive patient information and images in all diversity of the modalities and cases.

• About the DICOM standard

• Several links describing the DICOM file structure:

  A Very Basic DICOM Introduction

  Understanding DICOM

  More detailed file structure. Overview: Basic DICOM File Structure

• As finding required information in the original DICOM standard documentation is not very easy, one can use this handy DICOM Standard Browser

• A commonly used Python package to work with DICOM files is Pydicom

NIfTI

9 minutes to read

Another popular format to store medical data is NIfTI files. It is mainly used to store already anonymized and preprocessed volumetric data extracted from the studies.

• A quick introduction to the NIfTI-1.1 Data Format

• All the information is well-structured on the NIfTI format site (follow the links inside): About NIfTI format

• A commonly used Python package to work with NIfTI files is NiBabel

How the datasets are created

35 minutes to read

When a medical institution prepares the dataset, it follows a certain procedure, described in the paper Preparing Medical Imaging Data for Machine Learning.

Exercises

2 days of work

Do Exploratory Data Analysis (EDA) for the two datasets:

1. DICOM dataset

• Use dcmread function to read the files

• Use get() method or tag name as a field to access the values of the tags

• Use pixel_array field to access the image as a NumPy array

• Check out Dataset basics and Viewing images tutorials

2. NIfTI dataset

• Check out Getting started and Images and memory tutorials

Optional read

If you are already familiar with the general principles of obtaining images from different medical imaging apparatus, you can refresh your knowledge using the two slide decks:

• Medical Imaging Modalities: An Introduction

• Visual Medicine: Visual Medicine: Data Acquisition and Preprocessing

A book that will help you to deepen your knowledge about medical imaging: M. A. Flower “Webb’s Physics of Medical Imaging”, A TAYLOR & FRANCIS BOOK, ISBN 978-1-4665-6895-2