22,852 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
GATE : a simulation toolkit for PET and SPECT
Monte Carlo simulation is an essential tool in emission tomography that can
assist in the design of new medical imaging devices, the optimization of
acquisition protocols, and the development or assessment of image
reconstruction algorithms and correction techniques. GATE, the Geant4
Application for Tomographic Emission, encapsulates the Geant4 libraries to
achieve a modular, versatile, scripted simulation toolkit adapted to the field
of nuclear medicine. In particular, GATE allows the description of
time-dependent phenomena such as source or detector movement, and source decay
kinetics. This feature makes it possible to simulate time curves under
realistic acquisition conditions and to test dynamic reconstruction algorithms.
A public release of GATE licensed under the GNU Lesser General Public License
can be downloaded at the address http://www-lphe.epfl.ch/GATE/
3D-Cell-Annotator : an open-source active surface tool for single-cell segmentation in 3D microscopy images
aSummary: Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids and embryos) show that the precision of the segmentation reaches the level of a human expert.Peer reviewe
Computational medical imaging for total knee arthroplasty using visualitzation toolkit
This project is presented as a Master Thesis in the field of Civil Engineering, Biomedical specialization. As the
project of an Erasmus exchange student, this thesis has been under supervision both the Universite Livre de
Bruxelles and the Universitat Politecnica de Catalunya. The purpose of this thesis to put in practice all the
knowledges acquired during this Master in Industrial Engineering in UPC and to be a support for medical staff
in total knee arthoplasty procedures.
Prof. Emmanuel Thienpont has been working for years as orthopaedic surgeon at the Hospital Sant Luc,
Brussels. His years of work and research have been mainly focused on Total Knee Arthroplasty or TKA. During
one of the most important steps of this procedure, the orthopaedic surgeon has to cut the head of the femur
following two perpendicular cutting planes. Nevertheless, the orientation of these planes are directly dependant
of the femur constitution.
This Master Thesis has been conceived in order to offer the surgeon a tool to determine the proper direction
planes in a previous step before the surgical procedure. This project pretends to give the surgeon an openfree
computational platform to access to patient geometrical and physiological information before involving the
subject in any invasive procedure
J-PET Framework: Software platform for PET tomography data reconstruction and analysis
J-PET Framework is an open-source software platform for data analysis,
written in C++ and based on the ROOT package. It provides a common environment
for implementation of reconstruction, calibration and filtering procedures, as
well as for user-level analyses of Positron Emission Tomography data. The
library contains a set of building blocks that can be combined by users with
even little programming experience, into chains of processing tasks through a
convenient, simple and well-documented API. The generic input-output interface
allows processing the data from various sources: low-level data from the
tomography acquisition system or from diagnostic setups such as digital
oscilloscopes, as well as high-level tomography structures e.g. sinograms or a
list of lines-of-response. Moreover, the environment can be interfaced with
Monte Carlo simulation packages such as GEANT and GATE, which are commonly used
in the medical scientific community.Comment: 14 pages, 5 figure
Using high resolution displays for high resolution cardiac data
The ability to perform fast, accurate, high resolution visualization is fundamental
to improving our understanding of anatomical data. As the volumes of data
increase from improvements in scanning technology, the methods applied to rendering
and visualization must evolve. In this paper we address the interactive display of
data from high resolution MRI scanning of a rabbit heart and subsequent histological
imaging. We describe a visualization environment involving a tiled LCD panel
display wall and associated software which provide an interactive and intuitive user
interface.
The oView software is an OpenGL application which is written for the VRJuggler
environment. This environment abstracts displays and devices away from the
application itself, aiding portability between different systems, from desktop PCs to
multi-tiled display walls. Portability between display walls has been demonstrated
through its use on walls at both Leeds and Oxford Universities. We discuss important
factors to be considered for interactive 2D display of large 3D datasets,
including the use of intuitive input devices and level of detail aspects
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