Medical Image Analysis Laboratory

Welcome to the medical image analysis laboratory (MIALab). This repository contains all code you will need to get started with classical medical image analysis.

During the MIALab you will work on the task of brain tissue segmentation from magnetic resonance (MR) images (see data). We have set up an entire pipeline to solve this task, specifically:

• Pre-processing

• Registration

• Feature extraction

• Voxel-wise tissue classification

• Post-processing

• Evaluation

During the laboratory you will get to know the entire pipeline and investigate one of these pipeline elements in-depth (see pipeline). You will get to know and to use various libraries and software tools needed in the daily life as biomedical engineer or researcher in the medical image analysis domain (see tools).

Enjoy!

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Found a bug or do you have suggestions? Open an issue or better submit a pull request.

Getting started

• Installation
• Integrated Development Environment (IDE)
• Tools
• UBELIX HPC

Lecture notes

• Clinical Background
• Data
• Pipeline
• Pre-processing
• Registration
• Post-processing
• Feature Engineering
• Machine Learning

Packages

• Data (mialab.data package)
  • Structure (mialab.data.structure module)
• Filtering and manipulation (mialab.filtering package)
  • Pre-processing (mialab.filtering.preprocessing module)
  • Feature extraction (mialab.filtering.feature_extraction module)
  • Post-processing (mialab.filtering.postprocessing module)
• Utilities (mialab.utilities package)
  • The file access module (mialab.utilities.file_access_utilities)
  • The multi processor module (mialab.utilities.multi_processor)
  • The pipeline module (mialab.utilities.pipeline_utilities)

Indices

• Index

• Module Index