GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes

Larrabide, Ignacio; Omedas, Pedro; Martelli, Y.; Planes, X.; Nieber, Maarten; Moya, Juan A.; Butakoff, Constantine; Sebastián, Rafael; Cámara, Óscar; Craene, Mathieu De; Bijnens, Bart; Frangi, Alejandro F.

doi:10.1007/978-3-642-01932-6_45

Cited by 54 publications

(37 citation statements)

References 4 publications

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“…The 3D anatomical geometry was devel-oped by the Korea Institute of Science and Technology Information (KISTI) [11]. The geometry was decimated and prepared for simulation using the Graphical Interface for Medical Image Analysis and Simulation (GIMIAS) software developed by the Center for Computational Imaging and Simulation Technology in Biomedicine (CISTIB) at the Universitat Pompeu Fabra [12]. The main liver and vessels geometrical features are illustrated in table 1.…”

Section: Methodsmentioning

confidence: 99%

Impact of Liver Vasculature on Electric Field Distribution during Electroporation Treatments: An Anatomically Realistic Numerical Study

Qasrawi

Ivorra

2015

IFMBE Proceedings

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Abstract-Electroporation is the phenomenon in which cell membrane permeability is increased by exposing the cell to high intensity electric fields. In living tissues, such permeabilization boost can be used in order to enhance the penetration of drugs or DNA plasmids or to destroy undesirable cells and it is typically performed by applying pulsed high voltages across needle electrodes. When used for ablation, and particularly in the context of liver tumors, it is often claimed that in contrast with thermal ablation techniques, electroporation is not severely impacted by the presence of large blood vessels because the heat sinking characteristic of those is not relevant for the electric field distribution. However, blood vessels do distort the electric field distribution because of their high inner conductivity. The goal of the study presented here is to numerically analyze the relevance of such distortion in a clinical scenario. An anatomically realistic model of the liver and its vasculature within an abdominal section was implemented. The blood vessels ranged from 0.3 to 6.3 mm in diameter and from 24 to 68.56 mm in length. A series of simulations with plausible random locations and depths (needle tips from 10 to 25mm within the liver) for the electrode pairs was conducted. Locations and depths were carefully verified so that the electrodes did not penetrate the vessels. The results were compared to those assuming that liver tissue is homogeneous. These comparisons indicate that volume error caused by neglecting the presence of vessels is less than 3%, which can be considered negligible if compared to other error sources. However, it was noticed that if the treated region comprises vessels or is very close to them, undertreated and over treated spots will appear around the vessels. Since undertreated spots may imply that tumor cells remain viable after treatment, caution is advised.

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Section: Methodsmentioning

confidence: 99%

Impact of Liver Vasculature on Electric Field Distribution during Electroporation Treatments: An Anatomically Realistic Numerical Study

Qasrawi

Ivorra

2015

IFMBE Proceedings

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“…5 and animation in supplementary material). Visualization, segmentation and tracking were performed with GIMIAS v1.4.0 (Larrabide et al, 2009). Conversion to SSFP coordinates was done with DICOM header information.…”

Section: Ground-truth Landmarksmentioning

confidence: 99%

Benchmarking framework for myocardial tracking and deformation algorithms: An open access database

Tobon-Gómez

Craene

McLeod

et al. 2013

Medical Image Analysis

150

162

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In this paper we present a benchmarking framework for the validation of cardiac motion analysis algorithms. The reported methods are the response to an open challenge that was put to the medical imaging community through a MICCAI workshop. The database included magnetic resonance (MR) and 3D ultrasound (3DUS) datasets from a dynamic phantom and 15 healthy volunteers. Participants processed 3D tagged MR datasets (3DTAG), cine steady state free precession MR datasets (SSFP) and 3DUS datasets, amounting to 1158 image volumes. Ground-truth for motion tracking was based on 12 landmarks (4 walls at 3 ventricular levels). They were manually tracked by two observers in the 3DTAG data over the whole cardiac cycle, using an in-house application with 4D visualization capabilities. The median of the inter-observer variability was computed for the phantom dataset (0.77mm) and for the volunteer datasets (0.84mm). The ground-truth was registered to 3DUS coordinates using a point based similarity transform. Four institutions responded to the challenge by providing motion estimates for the data: Fraunhofer MEVIS (MEVIS), Bremen, Germany; Imperial College London -University College London (IUCL), UK; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Inria-Asclepios project (INRIA), France. Details on the implementation and evaluation of the four methodologies are presented in this manuscript. The manually tracked landmarks were used to evaluate tracking accuracy of all methodologies. For 3DTAG, median values were computed over all time frames for the phantom dataset (MEVIS=1.20mm, IUCL=0.73mm, UPF=1.10mm, INRIA=1.09mm) and for the volunteer datasets (MEVIS=1.33mm, IUCL=1.52mm, UPF=1.09mm, INRIA=1.32mm). For 3DUS, median values were computed at end diastole and end systole for the phantom dataset (MEVIS=4.40mm, UPF=3.48mm, INRIA=4.78mm) and for the volunteer datasets (MEVIS=3.51mm, UPF=3.71mm, INRIA=4.07mm). For SSFP, median values were computed at end diastole and end systole for the phantom dataset (UPF=6.18mm, INRIA=3.93mm) and for the volunteer datasets (UPF=3.09mm, INRIA=4.78mm). Finally, strain curves were generated and qualitatively compared. Good agreement was found between the different modalities and methodologies, except for radial strain that showed a high variability in cases of lower image quality.

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“…This medical application was developed using GIMIAS [4] GIMIAS relies on these libraries for visualization, user interaction, data access, image and mesh processing, and is designed to easily integrate proprietary algorithms and new libraries that broaden the functions of the framework. GIMIAS is currently collaborating to develop and adopt standards that could favour interoperability with similar software in the context of the VPHNoE [5].…”

Section: Methodsmentioning

confidence: 99%

QuantiDOPA: A Quantification Software for Dopaminergic Neurotransmission SPECT

et al. 2014

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Abstract-Quantification of neurotransmission Single-Photon Emission Computed Tomography (SPECT) studies of the dopaminergic system can be used to track, stage and facilitate early diagnosis of the disease. The aim of this study was to implement QuantiDOPA, a semi-automatic quantification software of application in clinical routine to reconstruct and quantify neurotransmission SPECT studies using radioligands which bind the dopamine transporter (DAT). To this end, a workflow oriented framework for the biomedical imaging (GIMIAS) was employed. QuantiDOPA allows the user to perform a semiautomatic quantification of striatal uptake by following three stages: reconstruction, normalization and quantification. QuantiDOPA is a useful tool for semi-automatic quantification in DAT SPECT imaging and it has revealed simple and flexible.

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GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes

Cited by 54 publications

References 4 publications

Impact of Liver Vasculature on Electric Field Distribution during Electroporation Treatments: An Anatomically Realistic Numerical Study

Impact of Liver Vasculature on Electric Field Distribution during Electroporation Treatments: An Anatomically Realistic Numerical Study

Benchmarking framework for myocardial tracking and deformation algorithms: An open access database

QuantiDOPA: A Quantification Software for Dopaminergic Neurotransmission SPECT

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