The Phenotyping

Table of Contents

• Tutorials
• Views
  • Specific Views:
  • Non-Specific Views:
• MiniApps (Command line Tools)

MITK Phenotyping is a selection of algorithms that can be used to extract image-based phenotypes, for example using a radiomics approach. The software is part of the research of the Division of Medical Image Computing of the German Cancer Research Center (DKFZ). MITK Phenotyping is not intended to be a single application, it is rather a collection of the necessary plugins within the offical MITK releases.

The functionality of MITK Phenotyping can be accessed in different ways: Using the graphical interface using the Plugins listed below, using command line applications, or using one of the programming interfaces.

Tutorials

• GUI based Radiomics Tutorial A tutorial on how to use the grapical interface of MITK Phenotying

Views

Specific Views:

Views that were developed with the main focus on Radiomics. They still might be used in other use-cases as well:

• Image Transformations : Image transformations like Resampling, Laplacian of Gaussian, and Wavelet Transformations
• Mask Processing : Processing and Cleaning of Masks
• Image Arithmetrics : Processing images using mathematical operations
• Radiomics Statistic : Calculate Radiomics Features

Non-Specific Views:

This section contains views that are included within MITK Phenotyping, but were developed with a broader application in mind.

• The Basic Image Processing : Deprecated plugin for performing different image-related tasks like subtraction, mutliplaction, filtering etc.
• The MatchPoint Algorithm Browser View : Selection of MatchPoint (Registration) Algorithm
• The MatchPoint Algorithm Control View : Configuring and Controlling MatchPoint (Registration) Algorithm
• The MatchPoint Registration Evaluation View : Evaluate the Registration performance using MatchPoint
• The MatchPoint Registration Manipulator View : Adapt a registration calculated using MatchPoint
• The MatchPoint Image Mapper View : Apply a MatchPoint Registration to a specific image
• The MatchPoint Registration Visualizer View : Visualize a Registration obtained with MatchPoint
• The Segmentation View : Creating Multilabel Segmentations
• The Segmentation Utilities View : Utilities for the processing of simple segmentations

MiniApps (Command line Tools)

• MITK MiniApps Explanation of the Command Line App concept in MITK
• MITK Basic Image Processing Mini Apps : List of common preprocessing MiniApps
• MITK Classification Mini Apps : (Incomplete) list of MITK Classification MiniApps