This document describes a suite of new multi-threaded classes for calculating magnetic resonance (MR) T2 and T1 parameter maps implemented using the Insight Toolkit ITK (www.itk.org). Similar to MR diffusion tensor imaging (DTI), MR T2 and T1 parameter maps provide a non-invasive means for quantitatively measuring disease or pathology in-vivo. Included in the suite are classes for reading proprietary Bruker 2dseq and Philips PAR/REC images and example programs and data for validating the new classes.

MR Parameter Map Suite: ITK Classes for Calculating Magnetic Resonance T2 and T1 Parameter Maps

This document describes a new class that takes an \doxygen{Transform} and
evaluates the deformation at points in a user-defined region.
The class is implemented using the Insight Toolkit url{www.itk.org}. \
This paper is accompanied with the source code, input data, parameters and
output data that the authors used for validating the algorithm described in
this paper.

Generating a Deformation Field from a Transform

Function Calls as Citations

In this article, we will present a novel interactive image registration technique using the 3D volumetric view as guidance throughout the registration process. The registration criterion used in this technique is the homogeneity of the color distribution on any given anatomic landmark, usually the skin/muscle voxels. This registration criterion has been validated using two different approaches, including comparison with automatic registration using mutual information based on the Insight Toolkits (ITK) and comparison with registered MR images with different pulse sequences acquired directly from the same MR scanner less than 5 minutes. An investigation is also made to compare this technique with the conventional interactive image registration using three orthogonal planar (3P) views, which is predominantly used in the current treatment planning in clinic. This 3D technique has shown several advantages, including improved registration accuracy and accelerated registration speed. It has also found that the 3P pixel registration technique often "inherits" a global positioning error, due to its partial 3D visual presentation. In addition, unlike the 3P technique, which generally cannot be used to register more than 2 images simultaneously and low resolution PET images, this 3D technique can register up to 4 imaging modalities simultaneously, including PET images, with both global view guidance and detail checking capability.

3D Voxel-Based Volumetric Image Registration with Volume-View Guidance

This paper focuses on the important role of open-source software in the development of a fully-automatic and accurate registration system for images of Quadrature Tomographic Microscopy. The system is correspondence-based, using the framework provided by open-source RGRL(Rensselear Generalized Registration Library). The library implements several well-known techniques and the ability to mix-and-match techniques for components of the framework allows testing of ideas and
development of the robust system in a timely fashion.

The Role of Open-Source Software in the Study of Embryogenesis

A novel fiber tracking algorithm (GTRACT) was developed to enhance tracking through ambiguous regions where cross fibers, fiber merging or fanning may be occurring. The software was developed using several cross platform open-source toolkits (ITK, VTK, and FLTK). The algorithm was evaluated using a freely available digital phantom dataset provided by King's College London. The results show that the GTRACT algorithm performed significantly better than standard streamline approaches and is less affected by noise.

Guided Diffusion Tensor Tractography with GTRACT: A Validation Study

The usage of image processing has become an important and continuous growing field in medical imaging. Although a large amount of algorithms is available, only few are routinely applied within applications for clinical diagnosis support and treatment planning. New tools are required that allow for efficient evaluation and comparison of algorithms as well as the 
generation of dedicated user interfaces with sophisticated visualization for clinical applications. We propose a generic integration of ITK algorithms into the visual programming and rapid prototyping platform MeVisLab. One of the main limitation of ITK is its lack of visualization and interaction functionality through a dedicated development platform. MeVisLab provides a modular visual programming interface with a comprehensive suite of image processing and visualization tools. The linkage of ITK algorithms to MeVisLab is based on a two step process that consists of a generic XML description for each ITK algorithm and an automatic code generator to create new MeVisLab modules, which will be made publicly available within the free version of MeVisLab. Each module can handle different image types and data dimensions dynamically at runtime. Example applications using registration, segmentation, and visualization modules are presented in order to show the capabilities of the described integration concept.

A Framework for Algorithm Evaluation and Clinical Application Prototyping using ITK

The Medical Imaging Interaction Toolkit (MITK) is an opensource toolkit for the development of interactive medical image analysis software. MITK is based on the open-source Insight Toolkit (ITK) and Visualization Toolkit (VTK) and extends them with features required for interactive systems. ITK is used for the algorithmic scope and general infrastructure, VTK for visualization. Key features of MITK are the coordination of multiple 2D and 3D visualizations of arbitrary data, a general interaction concept including undo/redo, and its extendibility and flexibility to create tailored applications due to its toolkit character and
different layers of hidden complexity. The paper gives a brief introduction into the overall concepts and goals of the MITK approach. Suggestions and participation are welcome. MITK is available at www.mitk.org.

The MITK Approach

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This ppt presentation discusses DeSci Labs' product, DeSci Publish. It includes a quick overview of the issues with the current states of research publishing and knowledge sharing that it is tackling, as well as the scope of what can be done with the product on several different levels, as well as a quick introduction into the tech background of its web3 embedding and new Novelty score features. 