Research of the Software development for Integrated Diagnostics and Therapy Group

RTToolbox

© dkfz.de

"RTToolbox" is a robust and flexible C++ software library developed to support quantitative analysis of treatment outcome for radiotherapy. It provides the import of radiotherapy data (e.g. plans, dose distributions and structure sets) in DICOM-RT standard format as well as in ITK supported data formats. Core features of the RTToolbox include: calculation of DVHs and dose comparison indices, and computation of radiobiological models (TCP/NTCP). Using the RTToolbox radiotherapy evaluation applications can be built easily and quickly.

 

 -> Clemens Hentschke

MatchPoint

MatchPoint is a translational registration framework: it eases the utilization of registration algorithms (own and external work) and their integration in arbitrary host applications. The concrete implementation of algorithmic components is not a focus of MatchPoint. Topics addressed by MatchPoint are registration algorithms as services and encapsulation of registration domain complexity among others. If you search for registration algorithms, you should look at projects like ITK, Plastimatch, Elastix ... . If you search for a framework that helps you to integrate (these) registration algorithms into your application, you are at the right place.

MatchPoint has implementations for different host applications. One freely available and recommended is the integration into MITK.

 

 -> Ralf Floca

AVID

The aim of AVID is to provide an open solution to orchestrate software components via workflow scripts. The main areas of application are scalable and flexible cohort analysis as well as variation effect and uncertainty quantification.

AVID is especially used in the context of radiotherapy. Therefore, many of the integrated components are provided by RT-Toolbox. However, it was also used successfully in other areas like radiological image analysis and image registration error effect studies.

 

 -> Ralf Floca

-> Clemens Hentschke

 

The Black Swan Project

© dkfz.de

This project is part of the “Black Swan Research Initiative”, launched by the International Myeloma Foundation. The goal is to establish an imaging based prognostic staging system for patients with multiple myeloma. In symptomatic patients focal lesions can be present in extensive numbers. The project aims to develop a set of automated detection, segmentation and characterization techniques for whole body image analysis. The system will quantify and assess the tumor mass trend over time.

 

-> Amir Kalali

CSI-HD

To make forensic radiology feasible, we develop workflows and processes that combine local and remote radiological infrastructure as well as latest technologies of medical image processing. To minimize required resources at image acquisition sites, we design automated image processing pipelines and secure data transfers to minimally occupy human resources and minimally interfere with previously existing on-site routine workflows.

This project is a cooperation between DKFZ, Institute for Legal and Traffic Medicine (University Clinic HD) and Institute for Anatomy (University HD)

 

 -> Ignaz Reicht

MITK-ModelFit and Perfusion

Model fitting plays a central role in the quantitative analysis of medical images. One prominent example is dynamic contrast-enhanced (DCE) MRI, where perfusion-related parameters are estimated using pharmacokinetic modelling. Other applications include mapping the apparent diffusion coefficient (ADC) in diffusion weighted MRI, and the analysis of Z-spectra in chemical exchange saturation transfer (CEST) imaging.

The ready-to-use model fitting toolbox is embedded into MITK and provides tools for model-fitting (ROI-based or voxel-by-voxel), fit evaluation and visualization. Any fitting task can be performed given a user-defined model. Being part of MITK, MITK-ModelFit applications can be easily and flexibly incorporated into pre-and post-processing workflows and offer a large set of interoperability options and supported data formats.

A special emphasis is put on pharmacokinetic analysis of DCE MRI data. Here, a variety of pharmacokinetic models is available. In addition tools are offered for arterial input function selection and conversion from signal to concentration.

-> Ralf Floca
-> Ina Kompan

MITK-MRUtilities

Magnetic Resonance imaging is moving towards ultra-high field strengths (7T and higher) to achieve higher resolutions, more enhanced image contrasts and an increased signal-to-noise-ratio. This provides the means for improved diagnostic methods and facilitates non-proton MRI such as sodium imaging. However, at ultra-high-field, physical and hardware limitations, such as RF field inhomogeneity, show as image distortions and artifacts. To overcome these limitations, novel pulse sequences, post-processing procedures and hardware extensions such parallel transmit coils are required.

The “MRUtilities”-toolbox is an extension of MITK which aims to support physicists and physicians conducting research at ultra-high field MRI. Provided applications include B1-mapping and optimized RF-shimming for parallel transmit coils.

-> Ina Kompan

Hyppopy

© dkfz.de

Hyppopy is a python toolbox for blackbox-function optimization providing an easy to use interface for a variety of solver frameworks. Hyppopy gives access to gridsearch, random and quasirandom, particle and bayes solvers. The aim of Hyppopy is making hyperparameter optimization as simple as possible (in our cases e.g. for the optimization of image processing pipelines or machine learning tasks). It can be easily integrated in existing code bases and provides real-time visualization of the parameter space and the optimization process via a visdom server. The internal design is focused on extensibility, ensuring that custom solver and future approaches can be integrated.

-> Ralf Floca

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