36 research outputs found
MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging -- design, implementation and application on the example of DCE-MRI
Many medical imaging techniques utilize fitting approaches for quantitative
parameter estimation and analysis. Common examples are pharmacokinetic modeling
in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and
Z-spectra analysis in chemical exchange saturation transfer MRI. Most available
software tools are limited to a special purpose and do not allow for own
developments and extensions. Furthermore, they are mostly designed as
stand-alone solutions using external frameworks and thus cannot be easily
incorporated natively in the analysis workflow. We present a framework for
medical image fitting tasks that is included in MITK, following a rigorous
open-source, well-integrated and operating system independent policy. Software
engineering-wise, the local models, the fitting infrastructure and the results
representation are abstracted and thus can be easily adapted to any model
fitting task on image data, independent of image modality or model. Several
ready-to-use libraries for model fitting and use-cases, including fit
evaluation and visualization, were implemented. Their embedding into MITK
allows for easy data loading, pre- and post-processing and thus a natural
inclusion of model fitting into an overarching workflow. As an example, we
present a comprehensive set of plug-ins for the analysis of DCE MRI data, which
we validated on existing and novel digital phantoms, yielding competitive
deviations between fit and ground truth. Providing a very flexible environment,
our software mainly addresses developers of medical imaging software that
includes model fitting algorithms and tools. Additionally, the framework is of
high interest to users in the domain of perfusion MRI, as it offers
feature-rich, freely available, validated tools to perform pharmacokinetic
analysis on DCE MRI data, with both interactive and automatized batch
processing workflows.Comment: 31 pages, 11 figures URL: http://mitk.org/wiki/MITK-ModelFi
Dynamic particle swarm optimization of biomolecular simulation parameters with flexible objective functions
Molecular simulations are a powerful tool to complement and interpret ambiguous experimental data on biomolecules to obtain structural models. Such data-assisted simulations often rely on parameters, the choice of which is highly non-trivial and crucial to performance. The key challenge is weighting experimental information with respect to the underlying physical model. We introduce FLAPS, a self-adapting variant of dynamic particle swarm optimization, to overcome this parameter selection problem. FLAPS is suited for the optimization of composite objective functions that depend on both the optimization parameters and additional, a priori unknown weighting parameters, which substantially influence the search-space topology. These weighting parameters are learned at runtime, yielding a dynamically evolving and iteratively refined search-space topology. As a practical example, we show how FLAPS can be used to find functional parameters for small-angle X-ray scattering-guided protein simulations
Feasibility and robustness of dynamic F-18-FET PET based tracer kinetic models applied to patients with recurrent high-grade glioma prior to carbon ion irradiation
The aim of this study was to analyze the robustness and diagnostic value of different compartment models for dynamic F-18-FET PET in recurrent high-grade glioma (HGG). Dynamic F-18-FET PET data of patients with recurrent WHO grade III (n:7) and WHO grade IV (n: 9) tumors undergoing re-irradiation with carbon ions were analyzed by voxelwise fitting of the time-activity curves with a simplified and an extended one-tissue compartment model (1TCM) and a two-tissue compartment model (2TCM), respectively. A simulation study was conducted to assess robustness and precision of the 2TCM. Parameter maps showed enhanced detail on tumor substructure. Neglecting the blood volume V-B in the 1TCM yields insufficient results. Parameter K-1 from both 1TCM and 2TCM showed correlation with overall patient survival after carbon ion irradiation (p = 0.043 and 0.036, respectively). The 2TCM yields realistic estimates for tumor blood volume, which was found to be significantly higher in WHO IV compared to WHO III (p = 0.031). Simulations on the 2TCM showed that K1 yields good accuracy and robustness while k(2) showed lowest stability of all parameters. The 1TCM provides the best compromise between parameter stability and model accuracy;however application of the 2TCM is still feasible and provides a more accurate representation of tracer-kinetics at the cost of reduced robustness. Detailed tracer kinetic analysis of F-18-FET PET with compartment models holds valuable information on tumor substructures and provides additional diagnostic and prognostic value
MONAI: An open-source framework for deep learning in healthcare
Artificial Intelligence (AI) is having a tremendous impact across most areas
of science. Applications of AI in healthcare have the potential to improve our
ability to detect, diagnose, prognose, and intervene on human disease. For AI
models to be used clinically, they need to be made safe, reproducible and
robust, and the underlying software framework must be aware of the
particularities (e.g. geometry, physiology, physics) of medical data being
processed. This work introduces MONAI, a freely available, community-supported,
and consortium-led PyTorch-based framework for deep learning in healthcare.
MONAI extends PyTorch to support medical data, with a particular focus on
imaging, and provide purpose-specific AI model architectures, transformations
and utilities that streamline the development and deployment of medical AI
models. MONAI follows best practices for software-development, providing an
easy-to-use, robust, well-documented, and well-tested software framework. MONAI
preserves the simple, additive, and compositional approach of its underlying
PyTorch libraries. MONAI is being used by and receiving contributions from
research, clinical and industrial teams from around the world, who are pursuing
applications spanning nearly every aspect of healthcare.Comment: www.monai.i