text:
.5, the trabeculations show similar complexity everywhere except for the anteroseptal and inferolateral area of the wall, where it is smaller. At 17.5 days, the regions of high complexity become more localized towards the inferoseptal and anterolateral parts of the wall. At 18.5 days, the high complexity area exhibits further localization at the inferoseptal and anterior part of the wall.},
author = {Paun, Bruno and Bijnens, Bart and Cook, Andrew C. and Mohun, Timothy J. and Butakoff, Constantine},
doi = {10.1016/j.media.2018.08.001},
issn = {13618423},
journal = {Medical Image Analysis},
keywords = {3D fractal analysis,Cardiac embryology,Cardiac morphogenesis,Cardiac trabeculations,High resolution episcopic microscopy},
pages = {89--104},
title = {{Quantification of the detailed cardiac left ventricular trabecular morphogenesis in the mouse embryo}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {49},
year = {2018}
}
@article{Payan2019,
abstract = {Purpose: The aim of this prospective study is to analyze the global tumor blood flow (BF) and its heterogeneity in newly diagnosed breast cancer (BC) according to tumor biological characteristics and molecular subtypes. These perfusion parameters were compared to those classically derived from metabolic studies to investigate links between perfusion and metabolism. Methods: Two hundred seventeen newly diagnosed BC patients underwent a 18F-FDG PET/CT exam before any treatment. A 2-min dynamic acquisition, centered on the chest, was performed immediately after intravenous injection of 3 MBq/kg of 18F-FDG, followed by a two-step static acquisition 90 min later. Tumor BF was calculated (in ml/min/g) using a single compartment kinetic model. In addition to standard PET parameters, texture features (TF) describing the heterogeneity of tumor perfusion and metabolism were extracted. Patients were divided into three groups: Luminal (HR+/HER2-), HER2 (HER2+), and TN (HR-/HER2-). Global and TF parameters of BF and metabolism were compared in different groups of patients according to tumor biological characteristics. Results: Tumors with lymph node involvement showed a higher perfusion, whereas no significant differences in SUV{\_}max or SUV{\_}mean were reported. TN tumors had a higher metabolic activity than HER2 and luminal tumors but no significant differences in global BF values were noted. HER2 tumors exhibited a larger tumor heterogeneity of both perfusion and metabolism compared to luminal and TN tumors. Heterogeneity of perfusion appeared well correlated to that of metabolism. Conclusions: The study of breast cancer perfusion shows a higher BF in large tumors and in tumors with lymph node involvement, not paralleled by similar modifications in tumor global metabolism. In addition, the observed correlation between the perfusion heterogeneity and the metabolism heterogeneity suggests that tumor perfusion and consequently the process of tumor angiogenesis might be involved in the metabolism heterogeneity previously shown in BC.},
author = {Payan, Neree and Presles, Benoit and Brunotte, Fran{\c{c}}ois and Coutant, Charles and Desmoulins, Isabelle and Vrigneaud, Jean Marc and Cochet, Alexandre},
doi = {10.1007/s00259-019-04422-4},
issn = {16197089},
journal = {European Journal of Nuclear Medicine and Molecular Imaging},
keywords = {18F-FDG PET/CT,Blood flow,Breast cancer,Heterogeneity,Textural features},
title = {{Biological correlates of tumor perfusion and its heterogeneity in newly diagnosed breast cancer using dynamic first-pass 18F-FDG PET/CT}},
type = {Journal Article},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85070290987{\&}doi=10.1007{\%}2Fs00259-019-04422-4{\&}partnerID=40{\&}md5=a6426041023e645a74b0ccede063cd2f},
year = {2019}
}
@article{Peng2008,
abstract = {In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called 'bioimage informatics'. This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools and other resources. {\textcopyright} 2008 The Author(s).},
author = {Peng, Hanchuan},
doi = {10.1093/bioinformatics/btn346},
issn = {13674803},
journal = {Bioinformatics},
number = {17},
pages = {1827--1836},
title = {{Bioimage informatics: A new area of engineering biology}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {24},
year = {2008}
}
@article{Pennati2014,
abstract = {Rationale and Objectives: The assessment of regional ventilation is of critical importance when investigating lung function during disease progression and planning of pulmonary interventions. Recently, different computed tomography (CT)-based parameters have been proposed as surrogates of lung ventilation. The aim of the present study was to compare these parameters, namely variations of density ($\delta$HU), specific volume (sVol), and specific gas volume ($\delta$SVg) between different lung volumes, in relation to their topographic distribution within the lung. Materials and Methods: Ten healthy volunteers were scanned via high-resolution CT at residual volume (RV) and total lung capacity (TLC); $\delta$HU, sVol, and $\delta$SVg were mapped voxel by voxel after registering TLC onto RV. Variations of the three parameters along the vertical and horizontal directions were analyzed. Results: Along the vertical direction (from ventral to dorsal regions), a strong dependence on gravity was found in $\delta$HU and sVol, with greater values in the dorsal regions of the lung (P{\textless}.001), whereas $\delta$SVg was more homogeneously distributed within the lung. Conversely, along the caudocranial direction (from lung bases to apexes) where no gravitational gradient is present, the three parameters behaved similarly, with lower values at the apices. Conclusions: $\delta$HU, sVol, and $\delta$SVg behave differently along the gravity direction. As the greater amount of air delivered to the dependent portion of the lung supplies a larger number of alveoli, the amount of gas delivered to alveoli compared to the mass of tissue is not gravity dependent. The minimization of gravity dependence in the distribution of ventilation when using $\delta$SVg suggests that this parameter is more reliable to discriminate healthy from pathologic regions.},
author = {Pennati, Francesca and Salito, Caterina and Baroni, Guido and Woods, Jason and Aliverti, Andrea},
doi = {10.1016/j.acra.2014.05.022},
issn = {18784046},
journal = {Academic Radiology},
keywords = {CT imaging,Gravity,Healthy lung,Ventilation},
number = {10},
pages = {1268--1275},
title = {{Comparison Between Multivolume CT-Based Surrogates of Regional Ventilation in Healthy Subjects}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {21},
year = {2014}
}
@article{Pheiffer2011,
abstract = {Modality-independent elastography (MIE) is a method of elastography that reconstructs the elastic properties of tissue using images acquired under different loading conditions and a biomechanical model. Boundary conditions are a critical input to the algorithm and are often determined by time-consuming point correspondence methods requiring manual user input. This study presents a novel method of automatically generating boundary conditions by nonrigidly registering two image sets with a demons diffusion-based registration algorithm. The use of this method was successfully performed in silico using magnetic resonance and X-ray-computed tomography image data with known boundary conditions. These preliminary results produced boundary conditions with an accuracy of up to 80 compared to the known conditions. Demons-based boundary conditions were utilized within a 3-D MIE reconstruction to determine an elasticity contrast ratio between tumor and normal tissue. Two phantom experiments were then conducted to further test the accuracy of the demons boundary conditions and the MIE reconstruction arising from the use of these conditions. Preliminary results show a reasonable characterization of the material properties on this first attempt and a significant improvement in the automation level and viability of the method. {\textcopyright} 2011 IEEE.},
author = {Pheiffer, Thomas S. and Ou, Jao J. and Ong, Rowena E. and Miga, Michael I.},
doi = {10.1109/TBME.2011.2159791},
issn = {00189294},
journal = {IEEE Transactions on Biomedical Engineering},
keywords = {Boundary conditions,elastography,finite element methods,image registration},
number = {9},
pages = {2607--2616},
title = {{Automatic generation of boundary conditions using demons nonrigid image registration for use in 3-D modality-independent elastography}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {58},
year = {2011}
}
@article{Phellan2018,
abstract = {Objective: Automatic vessel segmentation can be used to process the considerable amount of data generated by four-dimensional arterial spin labeling magnetic resonance angiography (4D ASL MRA) images. Previous segmentation approaches for dynamic series of images propose either reducing the series to a temporal average (tAIP) or maximum intensity projection (tMIP) prior to vessel segmentation, or a separate segmentation of each image. This paper introduces a method that combines both approaches to overcome the specific drawbacks of each technique. Methods: Vessels in the tAIP are enhanced by using the ranking orientation responses of path operators and multiscale vesselness enhancement filters. Then, tAIP segmentation is performed using a seed-based algorithm. In parallel, this algorithm is also used to segment each frame of the series and identify small vessels, which might have been lost in the tAIP segmentation. The results of each individual time frame segmentation are fused using an or boolean operation. Finally, small vessels found only in the fused segmentation are added to the tAIP segmentation. Results: In a quantitative analysis using ten 4D ASL MRA image series from healthy volunteers, the proposed combined approach reached an average Dice coefficient of 0.931, being more accurate than the corresponding tMIP, tAIP, and single time frame segmentation methods with statistical significance. Conclusion : The novel combined vessel segmentation strategy can be used to obtain improved vessel segmentation results from 4D ASL MRA and other dynamic series of images. Significance: Improved vessel segmentation of 4D ASL MRA allows a fast and accurate assessment of cerebrovascular structures.},
author = {Phellan, Renzo and Lindner, Thomas and Helle, Michael and Falcao, Alexandre X. and Forkert, Nils Daniel},
doi = {10.1109/TBME.2017.2759730},
issn = {15582531},
journal = {IEEE Transactions on Biomedical Engineering},
keywords = {Angiography,magnetic resonance angiography,temporal segmentation,vessel enhancement,vessel segmentation},
number = {7},
pages = {1486--1494},
title = {{Automatic Temporal Segmentation of Vessels of the Brain Using 4D ASL MRA Images}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {65},
year = {2018}
}
@incollection{Phellan2019,
abstract = {Medical imaging modalities, such as four-dimensional arterial spin label magnetic resonance angiography (4D ASL MRA), can acquire blood flow data of the cerebrovascular system. These datasets are useful to determine criteria of normality and diagnose, study, and follow-up on the treatment progress of cerebrovascular diseases. In particular, variations in the arterial transit time (ATT) are related to hemodynamic impairment as a consequence of vascular diseases. In order to obtain accurate ATT estimations, the acquisition parameters of the applied image modality need to be properly tuned. In case of 4D ASL MRA, two important acquisition parameters are the blood labeling duration and the temporal resolution. This paper evaluates the effect of different settings for the two mentioned parameters on the accuracy of the ATT estimation in 4D ASL MRA datasets. Six 4D ASL MRA datasets of a pipe containing a mixture of glycerine and water, circulated with constant flow rate using a pump, are acquired with different labeling duration and temporal resolution. A mathematical model is then fitted to the observed signal in order to estimate the ATT. The results indicate that the lowest average absolute error between the ground-truth and estimated ATT is achieved when the longest labeling duration of 1000 ms and the highest temporal resolution of 60 ms are used. The insight obtained from the experiments using a flow phantom, under controlled conditions, can be extended to tune acquisition parameters of 4D ASL MRA datasets of human subjects.},
author = {Phellan, Renzo and Lindner, Thomas and Helle, Michael and Falc{\~{a}}o, Alexandre X. and Forkert, Nils D.},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
doi = {10.1007/978-3-030-33327-0_17},
isbn = {9783030333263},
issn = {16113349},
keywords = {Arterial transit time,Blood flow,Hemodynamic analysis,Model fitting},
pages = {141--148},
title = {{The Effect of Labeling Duration and Temporal Resolution on Arterial Transit Time Estimation Accuracy in 4D ASL MRA Datasets - A Flow Phantom Study}},
type = {Serial},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075765108{\&}doi=10.1007{\%}2F978-3-030-33327-0{\_}17{\&}partnerID=40{\&}md5=34fc3b4595995b6c0ddd47325b464be7},
volume = {11794 LNCS},
year = {2019}
}
@article{Phillion2008,
abstract = {Semisolid tensile testing combined with X-ray microtomography (XMT) was used to characterize the development of internal damage as a function of strain in an aluminum-magnesium alloy, AA5182. Novel techniques were developed to allow the quantification of both the size evolution and orientation of the damage to determine mechanisms controlling the early stage growth and localization. During the initial stages of semisolid deformation, it was observed that strain was accommodated by both the growth of as-cast porosity and the detection of new damage-based voids. As the volume fraction of damage increases, the growth of voids occurs in an orientation perpendicular to the loading direction, both through expansion within the grain boundary liquid and void coalescence. The damage then localizes, causing failure. {\textcopyright} The Minerals, Metals {\&} Materials Society and ASM International 2008.},
author = {Phillion, Andre B. and Lee, P. D. and Maire, E. and Cockcroft, S. L.},
doi = {10.1007/s11661-008-9584-4},
issn = {10735623},
journal = {Metallurgical and Materials Transactions A: Physical Metallurgy and Materials Science},
number = {10},
pages = {2459--2469},
title = {{Quantitative assessment of deformation-induced damage in a Semisolid aluminum alloy via X-ray microtomography}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {39},
year = {2008}
}
@article{Pichat2018,
abstract = {Histology permits the observation of otherwise invisible structures of the internal topography of a specimen. Although it enables the investigation of tissues at a cellular level, it is invasive and breaks topology due to cutting. Three-dimensional (3D) reconstruction was thus introduced to overcome the limitations of single-section studies in a dimensional scope. 3D reconstruction finds its roots in embryology, where it enabled the visualisation of spatial relationships of developing systems and organs, and extended to biomedicine, where the observation of individual, stained sections provided only partial understanding of normal and abnormal tissues. However, despite bringing visual awareness, recovering realistic reconstructions is elusive without prior knowledge about the tissue shape. 3D medical imaging made such structural ground truths available. In addition, combining non-invasive imaging with histology unveiled invaluable opportunities to relate macroscopic information to the underlying microscopic properties of tissues through the establishment of spatial correspondences; image registration is one technique that permits the automation of such a process and we describe reconstruction methods that rely on it. It is thereby possible to recover the original topology of histology and lost relationships, gain insight into what affects the signals used to construct medical images (and characterise them), or build high resolution anatomical atlases. This paper reviews almost three decades of methods for 3D histology reconstruction from serial sections, used in the study of many different types of tissue. We first summarise the process that produces digitised sections from a tissue specimen in order to understand the peculiarity of the data, the associated artefacts and some possible ways to minimise them. We then describe methods for 3D histology reconstruction with and without the help of 3D medical imaging, along with methods of validation and some applications. We finally attempt to identify the trends and challenges that the field is facing, many of which are derived from the cross-disciplinary nature of the problem as it involves the collaboration between physicists, histolopathologists, computer scientists and physicians.},
author = {Pichat, Jonas and Iglesias, Juan Eugenio and Yousry, Tarek and Ourselin, S{\'{e}}bastien and Modat, Marc},
doi = {10.1016/j.media.2018.02.004},
issn = {13618423},
journal = {Medical Image Analysis},
keywords = {3D reconstruction,Histology,MRI,Medical imaging,Registration},
pages = {73--105},
title = {{A Survey of Methods for 3D Histology Reconstruction}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {46},
year = {2018}
}
@article{Pietzsch2012,
abstract = {ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixelalgebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins. {\textcopyright} 2012 The Author.},
author = {Pietzsch, Tobias and Preibisch, Stephan and Toman{\v{c}}{\'{a}}k, Pavel and Saalfeld, Stephan},
doi = {10.1093/bioinformatics/bts543},
issn = {14602059},
journal = {Bioinformatics},
number = {22},
pages = {3009--3011},
title = {{Img lib 2-generic image processing in Java}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {28},
year = {2012}
}
@article{Pinter2019,
abstract = {Background and objective: Segmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: conversion method selection, data provenance, data consistency, and coherence of in-memory objects. Methods: A complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable software tool to manage segmentation data in multiple data representations. A low-level core library called PolySeg implemented in the Visualization Toolkit (VTK) manages the data objects and conversions. It is used by a high-level application layer, which has been implemented in the medical image visualization and analysis platform 3D Slicer. The application layer provides advanced visualization, transformation, interoperability, and other functions. Results: The core conversion algorithms comprising the graph were validated. Several applications were implemented based on the library, demonstrating advantages in terms of usability and ease of software development in each case. The Segment Editor application provides fast, comprehensive, and easy-to-use manual and semi-automatic segmentation workflows. Clinical applications for gel dosimetry, external beam planning, and MRI-ultrasound image fusion in brachytherapy were rapidly prototyped resulting robust applications that are already in use in clinical research. The conversion algorithms were found to be accurate and reliable using these applications. Conclusions: A generic software library has been designed and developed for automatic management of multiple data formats in segmentation tasks. It enhances both user and developer experience, enabling fast and convenient manual workflows and quicker and more robust software prototyping. The software's BSD-style open-source license allows complete freedom of use of the library.},
author = {Pinter, Csaba and Lasso, Andras and Fichtinger, Gabor},
doi = {10.1016/j.cmpb.2019.02.011},
issn = {18727565},
journal = {Computer Methods and Programs in Biomedicine},
keywords = {3D Slicer,DICOM,Open-source,Segmentation,Software library,Voxelization},
pages = {19--26},
title = {{Polymorph segmentation representation for medical image computing}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {171},
year = {2019}
}
@article{Podlesek2015,
abstract = {Introduction: Ultrasound can visualize and update the vessel status in real time during cerebral vascular surgery. We studied the depiction of parent vessels and aneurysms with a high-resolution 3D intraoperative ultrasound imaging system during aneurysm clipping using rotational digital subtraction angiography as a reference. Methods: We analyzed 3D intraoperative ultrasound in 39 patients with cerebral aneurysms to visualize the aneurysm intraoperatively and the nearby vascular tree before and after clipping. Simultaneous coregistration of preoperative subtraction angiography data with 3D intraoperative ultrasound was performed to verify the anatomical assignment. Results: Intraoperative ultrasound detected 35 of 43 aneurysms (81{\%}) in 39 patients. Thirty-nine intraoperative ultrasound measurements were matched with rotational digital subtraction angiography and were successfully reconstructed during the procedure. In 7 patients, the aneurysm was partially visualized by 3D-ioUS or was not in field of view. Post-clipping intraoperative ultrasound was obtained in 26 and successfully reconstructed in 18 patients (69{\%}) despite clip related artefacts. The overlap between 3D-ioUS aneurysm volume and preoperative rDSA aneurysm volume resulted in a mean accuracy of 0.71 (Dice coefficient). Conclusions: Intraoperative coregistration of 3D intraoperative ultrasound data with preoperative rotational digital subtraction angiography is possible with high accuracy. It allows the immediate visualization of vessels beyond the microscopic field, as well as parallel assessment of blood velocity, aneurysm and vascular tree configuration. Although spatial resolution is lower than for standard angiography, the method provides an excellent vascular overview, advantageous interpretation of 3D-ioUS and immediate intraoperative feedback of the vascular status. A prerequisite for understanding vascular intraoperative ultrasound is image quality and a successful match with preoperative rotational digital subtraction angiography.},
author = {Podlesek, Dino and Meyer, Tobias and Morgenstern, Ute and Schackert, Gabriele and Kirsch, Matthias},
doi = {10.1371/journal.pone.0121345},
issn = {19326203},
journal = {PLoS ONE},
number = {3},
pages = {16},
title = {{Improved visualization of intracranial vessels with intraoperative coregistration of rotational digital subtraction angiography and intraoperative 3D ultrasound}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {10},
year = {2015}
}
@inbook{Polfliet2015,
abstract = {We present a method for automatically estimating prosthesis migration from previous and follow-up CT image data. The method consists of the segmentation of the bone and prosthesis in both images, followed by a registration of both substructures. The migration is found by computing the difference between both transforms. In this work we assess the accuracy of the method for zero migration. The method was applied on data from a mechanical phantom and on patient data, both with zero migration. Our experiments show that an accuracy of less than 0.3 mm can be achieved in a clinical setting.},
address = {Berlin},
author = {Polfliet, Mathias and Vandemeulebroucke, Jef and {Van Gompel}, Gert and Buls, Nico and Deklerck, Rudi and Scheerlinck, Thierry},
booktitle = {IFMBE Proceedings},
doi = {10.1007/978-3-319-11128-5_32},
editor = {Lackovic, I and Vasic, D},
isbn = {9783319111278},
issn = {16800737},
keywords = {Hip Prosthesis,Migration,Rigid Registration},
pages = {126--129},
publisher = {Springer-Verlag Berlin},
series = {IFMBE Proceedings},
title = {{Estimation of hip prosthesis migration: A study of zero migration}},
type = {Book Section},
url = {{\%}3CGo to},
volume = {45},
year = {2015}
}
@article{Poppe2019,
abstract = {Magma intrusions grow to their final geometries by deforming the Earth's crust internally and by displacing the Earth's surface. Interpreting the related displacements in terms of intrusion geometry is key to forecasting a volcanic eruption. While scaled laboratory models enable us to study the relationships between surface displacement and intrusion geometry, past approaches entailed limitations regarding imaging of the laboratory model interior or simplicity of the simulated crustal rheology. Here we apply cutting-edge medical wide beam X-ray Computed Tomography (CT) to quantify in 4D the deformation induced in laboratory models by an intrusion of a magma analog (golden syrup) into a rheologically-complex granular host rock analog (sand and plaster). We extract the surface deformation and we quantify the strain field of the entire experimental volume in 3D over time by using Digital Volume Correlation (DVC). By varying the strength and height of the host material, and intrusion velocity, we observe how intrusions of contrasting geometries grow, and induce contrasting strain field characteristics and surface deformation in 4D. The novel application of CT and DVC reveals that distributed strain accommodation and mixed-mode (opening and shear) fracturing dominates in low-cohesion material overburden, and leads to the growth of thick cryptodomes or cup-shaped intrusions. More localized strain accommodation and opening-mode fracturing dominates in high-cohesion material overburden, and leads to the growth of cone sheets or thin dikes. The results demonstrate how the combination of CT and DVC can greatly enhance the utility of optically non-transparent crustal rock analogs in obtaining insights into shallow crustal deformation processes. This unprecedented perspective on the spatio-temporal interaction of intrusion growth coupled with host material deformation provides a conceptual framework that can be tested by field observations at eroded volcanic systems and by the ever increasing spatial and temporal resolution of geodetic data at active volcanoes.},
author = {Poppe, Sam and Holohan, Eoghan P. and Galland, Olivier and Buls, Nico and {Van Gompel}, Gert and Keelson, Benyameen and Tournigand, Pierre Yves and Brancart, Joost and Hollis, Dave and Nila, Alex and Kervyn, Matthieu},
doi = {10.3389/feart.2019.00062},
issn = {22966463},
journal = {Frontiers in Earth Science},
keywords = {Analog,Digital volume correlation,Laboratory modeling,Magma intrusion,Surface deformation,X-ray computed tomography},
pages = {20},
title = {{An inside perspective on magma intrusion: Quantifying 3d displacement and strain in laboratory experiments by dynamic X-ray computed tomography}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {7},
year = {2019}
}
@article{Prasetio2018,
abstract = {The Vero linear accelerator delivers dynamic tumor tracking (DTT) treatment using a gimbal motion. However, the availability of treatment planning systems (TPS) to simulate DTT is limited. This study aims to implement and verify the gimbal tracking beam geometry in the dose calculation. Gimbal tracking was implemented by rotating the reference CT outside the TPS according to the ring, gantry, and gimbal tracking position obtained from the tracking log file. The dose was calculated using these rotated CTs. The geometric accuracy was verified by comparing calculated and measured film response using a ball bearing phantom. The dose was verified by comparing calculated 2D dose distributions and film measurements in a ball bearing and a homogeneous phantom using a gamma criterion of 2{\%}/2 mm. The effect of implementing the gimbal tracking beam geometry in a 3D patient data dose calculation was evaluated using dose volume histograms (DVH). Geometrically, the gimbal tracking implementation accuracy was {\textless}0.94 mm. The isodose lines agreed with the film measurement. The largest dose difference of 9.4{\%} was observed at maximum tilt positions with an isocenter and target separation of 17.51 mm. Dosimetrically, gamma passing rates were {\textgreater}98.4{\%}. The introduction of the gimbal tracking beam geometry in the dose calculation shifted the DVH curves by 0.05{\%}-1.26{\%} for the phantom geometry and by 5.59{\%} for the patient CT dataset. This study successfully demonstrates a method to incorporate the gimbal tracking beam geometry into dose calculations. By combining CT rotation and MU distribution according to the log file, the TPS was able to simulate the Vero tracking treatment dose delivery. The DVH analysis from the gimbal tracking dose calculation revealed changes in the dose distribution during gimbal DTT that are not visible with static dose calculations.},
author = {Prasetio, H. and W{\"{o}}lfelschneider, J. and Ziegler, M. and Serpa, M. and Witulla, B. and Bert, C.},
doi = {10.1088/1361-6560/aaa617},
issn = {13616560},
journal = {Physics in Medicine and Biology},
keywords = {MU distribution,dose reconstruction,dynamic tumor tracking,film dosimetry,gimbal tracking},
number = {3},
pages = {16},
title = {{Dose calculation and verification of the Vero gimbal tracking treatment delivery}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {63},
year = {2018}
}
@article{Price2017,
abstract = {Purpose: MR-only treatment planning requires images of high geometric fidelity, particularly for large fields of view (FOV). However, the availability of large FOV distortion phantoms with analysis software is currently limited. This work sought to optimize a modular distortion phantom to accommodate multiple bore configurations and implement distortion characterization in a widely implementable solution. Method and Materials: To determine candidate materials, 1.0 T MR and CT images were acquired of twelve urethane foam samples of various densities and strengths. Samples were precision-machined to accommodate 6 mm diameter paintballs used as landmarks. Final material candidates were selected by balancing strength, machinability, weight, and cost. Bore sizes and minimum aperture width resulting from couch position were tabulated from the literature (14 systems, 5 vendors). Bore geometry and couch position were simulated using MATLAB to generate machine-specific models to optimize the phantom build. Previously developed software for distortion characterization was modified for several magnet geometries (1.0 T, 1.5 T, 3.0 T), compared against previously published 1.0 T results, and integrated into the 3D Slicer application platform. Results: All foam samples provided sufficient MR image contrast with paintball landmarks. Urethane foam (compressive strength {\~{}}1000 psi, density {\~{}}20 lb/ft3) was selected for its accurate machinability and weight characteristics. For smaller bores, a phantomversion with the following parameters was used: 15 foam plates, 55 9 55 9 37.5 cm3 (L9W9H), 5,082 landmarks, and weight {\~{}}30 kg. To accommodate {\textgreater} 70 cm wide bores, an extended build used 20 plates spanning 55 9 55 9 50 cm3 with 7,497 landmarks and weight {\~{}}44 kg.Distortion characterization softwarewas implemented as an externalmodule into 3DSlicer's plugin framework and results agreed with the literature. Conclusion: The design and implementation of a modular, extendable distortion phantom was optimized for several bore configurations. The phantom and analysis software will be available for multi-institutional collaborations and cross-validation trials to support MR-only planning.},
author = {Price, Ryan G. and Knight, Robert A. and Hwang, Ken Pin and Bayram, Ersin and Nejad-Davarani, Siamak P. and Glide-Hurst, Carri K.},
doi = {10.1002/acm2.12090},
issn = {15269914},
journal = {Journal of Applied Clinical Medical Physics},
keywords = {Distortion,Gradient nonlinearity,MRI,Phantom,Spatial accuracy},
number = {4},
pages = {51--61},
title = {{Optimization of a novel large field of view distortion phantom for MR-only treatment planning}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {18},
year = {2017}
}
@article{Primpke2019,
abstract = {The ubiquitous presence of microlitter (ML), precisely microplastics (MP) and microfibres (MF) in the global environment is of growing concern for science, and society in general. Reliable methods are urgently needed for the identification and quantification of these emerging environmental pollutants. Recently a rapid Fourier transform infrared (FTIR) imaging pipeline was developed for automated identification and quantification of MP. However, although the usefulness for the quantification of MP could already be shown in several studies, microfibres could not be targeted so far by the developed analysis pipeline. In this study we present a novel approach for the simultaneous identification and quantification of MP and MF. By concentrating the sample on membrane filters and applying a BaF2 window on top of the filter, all objects-including MF-are fixed in the focal plane of the FTIR microscope. Furthermore, the analysis pipeline was augmented with algorithms which take into consideration the filamentous structure of MF. The novel analysis pipeline now allows to separate MP and MF via a preselection of fibres from the dataset by object size and shape. MP and MF are subsequently further investigated for specific polymer types and lengths/sizes. After parameter optimization the newly developed analysis approach was applied to archived samples from previous studies on treated waste water. The results were compared with respect to the original detected polymer types and numbers, but also considered MF detection.},
author = {Primpke, S. and Dias, P. A. and Gerdts, G.},
doi = {10.1039/c9ay00126c},
issn = {17599679},
journal = {Analytical Methods},
number = {16},
pages = {2138--2147},
title = {{Automated identification and quantification of microfibres and microplastics}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {11},
year = {2019}
}
@article{Primpke2017,
abstract = {The analysis of imaging data derived from micro-Fourier transform infrared ($\mu$FTIR) microscopy is a powerful tool allowing the analysis of microplastics enriched on membrane filters. In this study we present an automated approach to reduce the time demand currently needed for data analyses. We developed a novel analysis pipeline, based on the OPUS{\textcopyright} Software by Bruker, followed by image analysis with Python and Simple ITK image processing modules. By using this newly developed pipeline it was possible to analyse datasets from focal plane array (FPA) $\mu$FTIR mapping of samples containing up to 1.8 million single spectra. All spectra were compared against a database of different synthetic and natural polymers by various routines followed by benchmark tests with focus on accuracy and quality. The spectral correlation was optimized for high quality data generation, which allowed image analysis. Based on these results an image analysis approach was developed, providing information on particle numbers and sizes for each polymer detected. It was possible to collect all data with relative ease even for complex sample matrices. This approach significantly decreases the time demand for the interpretation of complex FTIR-imaging data and significantly increases the data quality.},
author = {Primpke, S. and Lorenz, C. and Rascher-Friesenhausen, R. and Gerdts, G.},
doi = {10.1039/c6ay02476a},
issn = {17599679},
journal = {Analytical Methods},
number = {9},
pages = {1499--1511},
title = {{An automated approach for microplastics analysis using focal plane array (FPA) FTIR microscopy and image analysis}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {9},
year = {2017}
}
@article{Primpke2018,
abstract = {The identification of microplastics becomes increasingly challenging with decreasing particle size and increasing sample heterogeneity. The analysis of microplastic samples by Fourier transform infrared (FTIR) spectroscopy is a versatile, bias-free tool to succeed at this task. In this study, we provide an adaptable reference database, which can be applied to single-particle identification as well as methods like chemical imaging based on FTIR microscopy. The large datasets generated by chemical imaging can be further investigated by automated analysis, which does, however, require a carefully designed database. The novel database design is based on the hierarchical cluster analysis of reference spectra in the spectral range from 3600 to 1250 cm−1. The hereby generated database entries were optimized for the automated analysis software with defined reference datasets. The design was further tested for its customizability with additional entries. The final reference database was extensively tested on reference datasets and environmental samples. Data quality by means of correct particle identification and depiction significantly increased compared to that of previous databases, proving the applicability of the concept and highlighting the importance of this work. Our novel database provides a reference point for data comparison with future and previous microplastic studies that are based on different databases. [Figure not available: see fulltext.].},
author = {Primpke, Sebastian and Wirth, Marisa and Lorenz, Claudia and Gerdts, Gunnar},
doi = {10.1007/s00216-018-1156-x},
issn = {16182650},
journal = {Analytical and Bioanalytical Chemistry},
keywords = {Database,FTIR,Imaging,Infrared,Microplastics,Spectroscopy},
number = {21},
pages = {5131--5141},
title = {{Reference database design for the automated analysis of microplastic samples based on Fourier transform infrared (FTIR) spectroscopy}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {410},
year = {2018}
}
@incollection{Pryamonosov2019,
abstract = {Segmentation of medical scans is the first and fundamental stage of numerical modeling of the human cardiovascular system. In this chapter, we analyze the results of coronary arteries segmentation using our approach for ten contrast-enhanced Computer Tomography Angiography datasets with different image quality and contrast phases. The segmentation is also affected by the patient anatomy, the shape and the scope of images. Our results show that the contrast phase timing is crucial for successful automatic segmentation. These factors form restrictions on the input data for automatic segmentation algorithms. Nevertheless, user guidance such as manual seeding and setting of thresholds can be used to significantly improve segmentation results and weaken the input restrictions.},
author = {Pryamonosov, Roman and Danilov, Alexander},
booktitle = {Smart Innovation, Systems and Technologies},
doi = {10.1007/978-3-030-06228-6_26},
isbn = {9783030062279},
issn = {21903026},
keywords = {Cardiovascular applications,Computed tomography,Contrast enhanced,Coronary arteries,Image segmentation,Personalized medicine},
pages = {331--344},
title = {{Robustness analysis of coronary arteries segmentation}},
type = {Serial},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85060769579{\&}doi=10.1007{\%}2F978-3-030-06228-6{\_}26{\&}partnerID=40{\&}md5=2732253554b40b79957430c0178be429},
volume = {133},
year = {2019}
}
@article{Punzo2016,
abstract = {Soon to be operational H I survey instruments such as APERTIF and ASKAP will produce large datasets. These surveys will provide information about the H I in and around hundreds of galaxies with a typical signal-to-noise ratio of ∼10 in the inner regions and ∼1 in the outer regions. In addition, such surveys will make it possible to probe faint H I structures, typically located in the vicinity of galaxies, such as extra-planar-gas, tails and filaments. These structures are crucial for understanding galaxy evolution, particularly when they are studied in relation to the local environment. Our aim is to find optimized kernels for the discovery of faint and morphologically complex H I structures. Therefore, using H I data from a variety of galaxies, we explore state-of-the-art filtering algorithms. We show that the intensity-driven gradient filter, due to its adaptive characteristics, is the optimal choice. In fact, this filter requires only minimal tuning of the input parameters to enhance the signal-to-noise ratio of faint components. In addition, it does not degrade the resolution of the high signal-to-noise component of a source. The filtering process must be fast and be embedded in an interactive visualization tool in order to support fast inspection of a large number of sources. To achieve such interactive exploration, we implemented a multi-core CPU (OpenMP) and a GPU (OpenGL) version of this filter in a 3D visualization environment (SlicerAstro).},
archivePrefix = {arXiv},
arxivId = {1609.03782},
author = {Punzo, D. and van der Hulst, J. M. and Roerdink, J. B.T.M.},
doi = {10.1016/j.ascom.2016.09.002},
eprint = {1609.03782},
issn = {22131337},
journal = {Astronomy and Computing},
keywords = {Radio lines: galaxies,Scientific visualization,Techniques: image processing},
pages = {163--176},
title = {{Finding faint H I structure in and around galaxies: Scraping the barrel}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {17},
year = {2016}
}
@article{Qiao2006,
abstract = {Cardiac and respiratory motion artefacts in PET imaging have been traditionally resolved by acquiring the data in gated mode. However, gated PET images are usually characterized by high noise content due to their low photon statistics. In this paper, we present a novel 4D model for the PET imaging system, which can incorporate motion information to generate a motion-free image with all acquired data. A computer simulation and a phantom study were conducted to test the performance of this approach. The computer simulation was based on a digital phantom that was continuously scaled during data acquisition. The phantom study, on the other hand, used two spheres in a tank of water, all of which were filled with 18F water. One of the spheres was stationary while the other moved in a sinusoidal fashion to simulate tumour motion in the thorax. Data were acquired using both 4D CT and gated PET. Motion information was derived from the 4D CT images and then used in the 4D PET model. Both studies showed that this 4D PET model had a good motion-compensating capability. In the phantom study, this approach reduced quantification error of the radioactivity concentration by 95{\%} when compared to a corresponding static acquisition, while signal-to-noise ratio was improved by 210{\%} when compared to a corresponding gated image. {\textcopyright} 2006 IOP Publishing Ltd.},
author = {Qiao, Feng and Pan, Tinsu and Clark, John W. and Mawlawi, Osama R.},
doi = {10.1088/0031-9155/51/15/012},
issn = {00319155},
journal = {Physics in Medicine and Biology},
number = {15},
pages = {3769--3783},
title = {{A motion-incorporated reconstruction method for gated PET studies}},
type = {Journal Article},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33746512521{\&}doi=10.1088{\%}2F0031-9155{\%}2F51{\%}2F15{\%}2F012{\&}partnerID=40{\&}md5=85744da7c87fdff0c273cb687cee3723},
volume = {51},
year = {2006}
}
@article{Qiao2007,
abstract = {A motion-incorporated reconstruction (MIR) method for gated PET imaging has recently been developed by several authors to correct for respiratory motion artifacts in PET imaging. This method however relies on a motion map derived from images (4D PET or 4D CT) of the entire field of view (FOV). In this study we present a region of interest (ROI)-based extension to this method, whereby only the motion map of a user-defined ROI is required and motion incorporation during image reconstruction is solely performed within the ROI. A phantom study and an NCAT computer simulation study were performed to test the feasibility of this method. The phantom study showed that the ROI-based MIR produced results that are within 1.26{\%} of those obtained by the full image-based MIR approach when using the same accurate motion information. The NCAT phantom study on the other hand, further verified that motion of features of interest in an image can be estimated more efficiently and potentially more accurately using the ROI-based approach. A reduction of motion estimation time from 450 s to 30 and 73 s was achieved for two different ROIs respectively. In addition, the ROI-based approach showed a reduction in registration error of 43{\%} for one ROI, which effectively reduced quantification bias by 44{\%} and 32{\%} using mean and maximum voxel values, respectively. {\textcopyright} 2007 IOP Publishing Ltd.},
author = {Qiao, Feng and Pan, Tinsu and Clark, John W. and Mawlawi, Osama R.},
doi = {10.1088/0031-9155/52/10/003},
issn = {00319155},
journal = {Physics in Medicine and Biology},
number = {10},
title = {{Region of interest motion compensation for PET image reconstruction}},
type = {Journal Article},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34248204627{\&}doi=10.1088{\%}2F0031-9155{\%}2F52{\%}2F10{\%}2F003{\&}partnerID=40{\&}md5=deb8145b579395e0ef985aab49663666},
volume = {52},
year = {2007}
}
@article{Qu2015,
abstract = {Warping images into a standard coordinate space is critical for many image computing related tasks. However, for multi-dimensional and high-resolution images, an accurate warping operation itself is often very expensive in terms of computer memory and computational time. For high-throughput image analysis studies such as brain mapping projects, it is desirable to have high performance image warping tools that are compatible with common image analysis pipelines. In this article, we present LittleQuickWarp, a swift and memory efficient tool that boosts 3D image warping performance dramatically and at the same time has high warping quality similar to the widely used thin plate spline (TPS) warping. Compared to the TPS, LittleQuickWarp can improve the warping speed 2-5 times and reduce the memory consumption 6-20 times. We have implemented LittleQuickWarp as an Open Source plug-in program on top of the Vaa3D system (http://vaa3d.org). The source code and a brief tutorial can be found in the Vaa3D plugin source code repository.},
author = {Qu, Lei and Peng, Hanchuan},
doi = {10.1016/j.ymeth.2014.09.002},
issn = {10959130},
journal = {Methods},
keywords = {B-spline,Image registration,Thin plate spline,Warping},
pages = {38--42},
title = {{LittleQuickWarp: An ultrafast image warping tool}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {73},
year = {2015}
}
@article{Rak2017,
abstract = {Purpose: In interstitial high-dose rate brachytherapy, liver cancer is treated by internal radiation, requiring percutaneous placement of applicators within or close to the tumor. To maximize utility, the optimal applicator configuration is pre-planned on magnetic resonance images. The pre-planned configuration is then implemented via a magnetic resonance-guided intervention. Mapping the pre-planning information onto interventional data would reduce the radiologist's cognitive load during the intervention and could possibly minimize discrepancies between optimally pre-planned and actually placed applicators. Methods: We propose a fast and robust two-step registration framework suitable for interventional settings: first, we utilize a multi-resolution rigid registration to correct for differences in patient positioning (rotation and translation). Second, we employ a novel iterative approach alternating between bias field correction and Markov random field deformable registration in a multi-resolution framework to compensate for non-rigid movements of the liver, the tumors and the organs at risk. In contrast to existing pre-correction methods, our multi-resolution scheme can recover bias field artifacts of different extents at marginal computational costs. Results: We compared our approach to deformable registration via B-splines, demons and the SyN method on 22 registration tasks from eleven patients. Results showed that our approach is more accurate than the contenders for liver as well as for tumor tissues. We yield average liver volume overlaps of 94.0 ± 2.7{\%} and average surface-to-surface distances of 2.02 ± 0.87 mm and 3.55 ± 2.19 mm for liver and tumor tissue, respectively. The reported distances are close to (or even below) the slice spacing (2.5 – 3.0 mm) of our data. Our approach is also the fastest, taking 35.8 ± 12.8 s per task. Conclusion: The presented approach is sufficiently accurate to map information available from brachytherapy pre-planning onto interventional data. It is also reasonably fast, providing a starting point for computer-aidance during intervention.},
author = {Rak, Marko and K{\"{o}}nig, Tim and T{\"{o}}nnies, Klaus D. and Walke, Mathias and Ricke, Jens and Wybranski, Christian},
doi = {10.1007/s11548-017-1633-2},
issn = {18616429},
journal = {International Journal of Computer Assisted Radiology and Surgery},
keywords = {Bias field correction,Deformable registration,High-dose rate brachytherapy,Liver intervention,Magnetic resonance imaging},
number = {12},
pages = {2169--2180},
title = {{Joint deformable liver registration and bias field correction for MR-guided HDR brachytherapy}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {12},
year = {2017}
}
@article{Ramirez2011,
abstract = {Subcortical hyperintensities (SH) are a commonly observed phenomenon on MRI of the aging brain (Kertesz et al., 1988). Conflicting behavioral, cognitive and pathological associations reported in the literature underline the need to develop an intracranial volumetric analysis technique to elucidate pathophysiological origins of SH in Alzheimer's disease (AD), vascular cognitive impairment (VCI) and normal aging (De Leeuw et al., 2001; Mayer and Kier, 1991; Pantoni and Garcia, 1997; Sachdev et al., 2008). The challenge is to develop processing tools that effectively and reliably quantify subcortical small vessel disease in the context of brain tissue compartments. Segmentation and brain region parcellation should account for SH subtypes which are often classified as: periventricular (pvSH) and deep white (dwSH), incidental white matter disease or lacunar infarcts and Virchow-Robin spaces. Lesion Explorer (LE) was developed as the final component of a comprehensive volumetric segmentation and parcellation image processing stream built upon previously published methods (Dade et al., 2004; Kovacevic et al., 2002). Inter-rater and inter-method reliability was accomplished both globally and regionally. Volumetric analysis showed high inter-rater reliability both globally (ICC = 99) and regionally (ICC = 98). Pixel-wise spatial congruence was also high (SI = 97). Whole brain pvSH volumes yielded high inter-rater reliability (ICC = 99). Volumetric analysis against an alternative kNN segmentation revealed high inter-method reliability (ICC = 97). Comparison with visual rating scales showed high significant correlations (ARWMC: r = 86; CHIPS: r = 87). The pipeline yields a comprehensive and reliable individualized volumetric profile for subcortical vasculopathy that includes regionalized (26 brain regions) measures for: GM, WM, sCSF, vCSF, lacunar and non-lacunar pvSH and dwSH. {\textcopyright} 2010 Elsevier Inc.},
author = {Ramirez, J. and Gibson, E. and Quddus, A. and Lobaugh, N. J. and Feinstein, A. and Levine, B. and Scott, C. J.M. and Levy-Cooperman, N. and Gao, F. Q. and Black, S. E.},
doi = {10.1016/j.neuroimage.2010.09.013},
issn = {10538119},
journal = {NeuroImage},
keywords = {Aging,Alzheimer's disease,Brain volume,Lesion analysis,Leukoariosis,MRI,Segmentation,White matter hyperintensities},
number = {2},
pages = {963--973},
title = {{Lesion Explorer: A comprehensive segmentation and parcellation package to obtain regional volumetrics for subcortical hyperintensities and intracranial tissue}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {54},
year = {2011}
}
@article{Ramirez2018,
abstract = {Open science, as a common good, opens possibilities for the development of nations, through innovations and collaborative constructions, which help to democratize knowledge. Advances in this area are still emerging, and the open science, co-creation of knowledge and open innovation triangle, is presented as an opportunity to generate an original contribution from research to open educational theory and practices. The study analyzed the articles that addressed this triangle, in order to identify the contexts and challenges that arise in open innovation and the co-creation of knowledge to promote open science. The method was a systematic literature review (SLR) of 168 articles published in open access format, from January 2014 to May 2017 in the Web of Science and Scopus databases. In the validation process, the York University criteria were used: inclusion and exclusion, relevance of the pertinent studies, evaluation of the quality / validity of included studies and description of data / basic studies. The findings showed that the most-widely publicized contexts were in the United States and Brazil, in the business and academic sectors (closely followed by the social sector), and the challenges were open to innovation, opening and research. The research concludes that the context and practices of collaboration are substantial elements for innovation and open science.},
author = {Ram{\'{i}}rez, Mar{\'{i}}a Soledad and Garc{\'{i}}a-Pe{\~{n}}alvo, Francisco Jos{\'{e}}},
doi = {10.3916/C54-2018-01},
issn = {19883293},
journal = {Comunicar},
keywords = {Citizen science,Collaboration,Innovation,Knowledge,Knowledge co-creation,Open science,Openness,Validation},
number = {54},
pages = {9--18},
title = {{Co-creation and open innovation: Systematic literature review}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {26},
year = {2018}
}
@article{Rasmussen2007,
abstract = {Objective. The aims of this study were: 1) To develop protocols for, integration and assessment of the usefulness of high quality fMRI (functional magnetic resonance imaging) and DTI (diffusion tensor imaging) data in an ultrasound-based neuronavigation system. 2) To develop and demonstrate a co-registration method for automatic brain-shift correction of pre-operative MR data using intra-operative 3D ultrasound. Methods. Twelve patients undergoing brain surgery were scanned to obtain structural and fMRI data before the operation. In six of these patients, DTI data was also obtained. The preoperative data was imported into a commercial ultrasound-based navigation system and used for surgical planning and guidance. Intra-operative ultrasound volumes were acquired when needed during surgery and the multimodal data was used for guidance and resection control. The use of the available image information during planning and surgery was recorded. An automatic voxel-based registration method between preoperative MRA and intra-operative 3D ultrasound angiography (Power Doppler) was developed and tested postoperatively. Results. The study showed that it is possible to implement robust, high-quality protocols for fMRI and DTI and that the acquired data could be seamlessly integrated in an ultrasound-based neuronavigation system. Navigation based on fMRI data was found to be important for pre-operative planning in all twelve procedures. In five out of eleven cases the data was also found useful during the resection. DTI data was found to be useful for planning in all five cases where these data were imported into the navigation system. In two out of four cases DTI data was also considered important during the resection (in one case DTI data were acquired but not imported and in another case fMRI and DTI data could only be used for planning). Information regarding the location of important functional areas (fMRI) was more beneficial during the planning phase while DTI data was more helpful during the resection. Furthermore, the surgeon found it more user-friendly and efficient to interpret fMRI and DTI information when shown in a navigation system as compared to the traditional display on a light board or monitor. Updating MRI data for brain-shift using automatic co-registration of preoperative MRI with intra-operative ultrasound was feasible. Conclusion. In the present study we have demonstrated how both fMRI and DTI data can be acquired and integrated into a neuronavigation system for improved surgical planning and guidance. The surgeons reported that the integration of fMRI and DTI data in the navigation system represented valuable additional information presented in a user-friendly way and functional neuronavigation is now in routine use at our hospital. Furthermore, the present study showed that automatic ultrasound-based updates of important pre-operative MRI data are feasible and hence can be used to compensate for brain shift. {\textcopyright} 2007 Springer-Verlag.},
author = {Rasmussen, I. A. and Lindseth, F. and Rygh, O. M. and Berntsen, E. M. and Selbekk, T. and Xu, J. and {Nagelhus Hernes}, T. A. and Harg, E. and H{\aa}berg, A. and Unsgaard, G.},
doi = {10.1007/s00701-006-1110-0},
issn = {00016268},
journal = {Acta Neurochirurgica},
keywords = {Brain shift,Diffusion tensor imaging,Functional magnetic resonance imaging,Image guidance,Image registration,Intra-operative 3D ultrasound,Minimally invasive surgery,Multimodal imaging,Neuronavigation},
number = {4},
pages = {365--378},
title = {{Functional neuronavigation combined with intra-operative 3D ultrasound: Initial experiences during surgical resections close to eloquent brain areas and future directions in automatic brain shift compensation of preoperative data}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {149},
year = {2007}
}
@article{Raudaschl2010,
abstract = {Purpose The favored treatment for many hip fractures is a sliding hip screw, and its usage is expected to increase in the future.Failures can be reduced, and complications detected earlier by semi-automated CT image analysis.The most frequent failure is due to the screw cut-out from the femoral head.Methods An image-based method was developed for early detection of complications and assessment of anchorage quality relative to implant model, bone quality or tip-apex distance (TAD).This method evaluates micro-migration using CT images acquired at different time points (immediately post-op and 3-month later).Serial CT image registration and transformation methods were applied, including point-based registration, to achieve semi-automated evaluations.Results Qualitative and quantitative validation of the image registration was performed with measurement mean error determination by different observers.The micro-migration evaluation by clinicians compared favorably with semiautomated image-based results.Conclusion Semi-automatic evaluation of hip screw micromigration using CT images is feasible and can aid observation of convalescence.The method may be amenable to full automation, a future goal for this work. {\textcopyright} CARS 2010.},
author = {Raudaschl, Patrik and Fritscher, Karl and Roth, Tobias and Kammerlander, Christian and Schubert, Rainer},
doi = {10.1007/s11548-010-0498-4},
issn = {18616429},
journal = {International Journal of Computer Assisted Radiology and Surgery},
keywords = {Cut-out,Hip fractures,Micro-migration,Sliding hip screw},
number = {5},
pages = {455--460},
title = {{Analysis of the micro-migration of sliding hip screws by using point-based registration}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {5},
year = {2010}
}
@article{Rautek2014,
abstract = {Researchers from many domains use scientific visualization in their daily practice. Existing implementations of algorithms usually come with a graphical user interface (high-level interface), or as software library or source code (low-level interface). In this paper we present a system that integrates domain-specific languages (DSLs) and facilitates the creation of new DSLs. DSLs provide an effective interface for domain scientists avoiding the difficulties involved with low-level interfaces and at the same time offering more flexibility than high-level interfaces. We describe the design and implementation of ViSlang, an interpreted language specifically tailored for scientific visualization. A major contribution of our design is the extensibility of the ViSlang language. Novel DSLs that are tailored to the problems of the domain can be created and integrated into ViSlang. We show that our approach can be added to existing user interfaces to increase the flexibility for expert users on demand, but at the same time does not interfere with the user experience of novice users. To demonstrate the flexibility of our approach we present new DSLs for volume processing, querying and visualization. We report the implementation effort for new DSLs and compare our approach with Matlab and Python implementations in terms of run-time performance.},
author = {Rautek, Peter and Bruckner, Stefan and Gr{\"{o}}ller, M. Eduard and Hadwiger, Markus},
doi = {10.1109/TVCG.2014.2346318},
issn = {10772626},
journal = {IEEE Transactions on Visualization and Computer Graphics},
keywords = {Domain-specific languages,Volume visualization,Volume visualization framework},
number = {12},
pages = {2388--2396},
title = {{ViSlang: A system for interpreted domain-specific languages for scientific visualization}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {20},
year = {2014}
}
@article{Reckfort2015,
abstract = {Structural connectivity of the brain can be conceptionalized as a multiscale organization. The present study is built on 3D-Polarized Light Imaging (3D-PLI), a neuroimaging technique targeting the reconstruction of nerve fiber orientations and therefore contributing to the analysis of brain connectivity. Spatial orientations of the fibers are derived from birefringence measurements of unstained histological sections that are interpreted by means of a voxel-based analysis. This implies that a single fiber orientation vector is obtained for each voxel, which reflects the net effect of all comprised fibers. We have utilized two polarimetric setups providing an object space resolution of 1.3 $\mu$m/px (microscopic setup) and 64 $\mu$m/px (macroscopic setup) to carry out 3D-PLI and retrieve fiber orientations of the same tissue samples, but at complementary voxel sizes (i.e., scales). The present study identifies the main sources which cause a discrepancy of the measured fiber orientations observed when measuring the same sample with the two polarimetric systems. As such sources the differing optical resolutions and diverging retardances of the implemented waveplates were identified. A methodology was implemented that enables the compensation of measured different systems' responses to the same birefringent sample. This opens up new ways to conduct multiscale analysis in brains by means of 3D-PLI and to provide a reliable basis for the transition between different scales of the nerve fiber architecture.},
author = {Reckfort, Julia and Wiese, Hendrik and Pietrzyk, Uwe and Zilles, Karl and Amunts, Katrin and Axer, Markus},
doi = {10.3389/fnana.2015.00118},
issn = {16625129},
journal = {Frontiers in Neuroanatomy},
keywords = {Brain,Connectome,Fiber orientation,Multiscale approach,Polarized light imaging},
number = {september},
pages = {11},
title = {{A multiscale approach for the reconstruction of the fiber architecture of the human brain based on 3D-PLI}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {9},
year = {2015}
}
@article{Reitz2008,
abstract = {Accurate daily patient localization is becoming increasingly important in external-beam radiotherapy (RT). Mega-voltage cone-beam computed tomography (MV-CBCT) utilizing a therapy beam and an on-board electronic portal imager can be used to localize tumor volumes and verify the patient's position prior to treatment. MV-CBCT produces a static volumetric image and therefore can only account for inter-fractional changes. In this work, the feasibility of using the MV-CBCT raw data as a fluoroscopic series of portal images to monitor tumor changes due to e.g. respiratory motion was investigated. A method was developed to read and convert the CB raw data into a cine. To improve the contrast-to-noise ratio on the MV-CB projection data, image post-processing with filtering techniques was investigated. Volumes of interest from the planning CT were projected onto the MV-cine. Because of the small exposure and the varying thickness of the patient depending on the projection angle, soft-tissue contrast was limited. Tumor visibility as a function of tumor size and projection angle was studied. The method was well suited in the upper chest, where motion of the tumor as well as of the diaphragm could be clearly seen. In the cases of patients with non-small cell lung cancer with medium or large tumor masses, we verified that the tumor mass was always located within the PTV despite respiratory motion. However for small tumors the method is less applicable, because the visibility of those targets becomes marginal. Evaluation of motion in non-superior-inferior directions might also be limited for small tumor masses. Viewing MV-CBCT data in a cine mode adds to the utility of MV-CBCT for verification of tumor motion and for deriving individualized treatment margins. {\textcopyright} 2008 Institute of Physics and Engineering in Medicine.},
author = {Reitz, Bodo and Gayou, Olivier and Parda, David S. and Miften, Moyed},
doi = {10.1088/0031-9155/53/4/001},
issn = {00319155},
journal = {Physics in Medicine and Biology},
number = {4},
pages = {823--836},
title = {{Monitoring tumor motion with on-line mega-voltage cone-beam computed tomography imaging in a cine mode}},
type = {Journal Article},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-39049165539{\&}doi=10.1088{\%}2F0031-9155{\%}2F53{\%}2F4{\%}2F001{\&}partnerID=40{\&}md5=1053838180560cce8431007aee909ef5},
volume = {53},
year = {2008}
}
@article{Riddle2011,
abstract = {Objective: Although magnetic resonance imaging (MRI) is the optimal imaging modality to define cerebral white-matter injury (WMI) in preterm survivors, the histopathological features of MRI-defined chronic lesions are poorly defined. We hypothesized that chronic WMI is related to a combination of delayed oligodendrocyte (OL) lineage cell death and arrested maturation of preoligodendrocytes (preOLs). We determined whether ex vivo MRI can distinguish distinct microglial and astroglial responses related to WMI progression and arrested preOL differentiation. Methods: We employed a preterm fetal sheep model of global cerebral ischemia in which acute WMI results in selective preOL degeneration. We developed novel algorithms to register histopathologically- defined lesions with contrast-weighted and diffusion-weighted high-field ex vivo MRI data. Results: Despite mild delayed preOL degeneration, preOL density recovered to control levels by 7 days after ischemia and was {\^{a}}2 fold greater at 14 days. However, premyelinating OLs were significantly diminished at 7 and 14 days. WMI evolved to mostly gliotic lesions where arrested preOL differentiation was directly proportional to the magnitude of astrogliosis. A reduction in cerebral WM volume was accompanied by four classes of MRI-defined lesions. Each lesion type displayed unique astroglial and microglial responses that corresponded to distinct forms of necrotic or non-necrotic injury. High-field MRI defined 2 novel hypointense signal abnormalities on T 2-weighted images that coincided with microscopic necrosis or identified astrogliosis with high sensitivity and specificity. Interpretation: These studies support the potential of high-field MRI for early identification of microscopic necrosis and gliosis with preOL maturation arrest, a common form of WMI in preterm survivors. {\textcopyright} 2011 American Neurological Association.},
author = {Riddle, Art and Dean, Justin and Buser, Joshua R. and Gong, Xi and Maire, Jennifer and Chen, Kevin and Ahmad, Tahir and Cai, Victor and Nguyen, Thuan and Kroenke, Christopher D. and Hohimer, A. Roger and Back, Stephen A.},
doi = {10.1002/ana.22501},
issn = {03645134},
journal = {Annals of Neurology},
number = {3},
pages = {493--507},
title = {{Histopathological correlates of magnetic resonance imaging-defined chronic perinatal white matter injury}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {70},
year = {2011}
}
@article{Riedel2010,
abstract = {Background and Purpose-: We sought to evaluate how accurately length and volume of thrombotic clots occluding cerebral arteries of patients with acute ischemic stroke can be assessed from nonenhanced CT (NECT) scans reconstructed with different slice widths. Methods-: NECT image data of 58 patients with acute ischemic stroke with vascular occlusion proven by CT angiography were reconstructed with slice widths of 1.25 mm, 2.5 mm, 3.75 mm, and 5 mm. Thrombus lengths and volumes were quantified based on these NECT images by detecting and segmenting intra-arterial hyperdensities. The results were compared with reference values of thrombus length and volume obtained from CT angiography images using Bland-Altman analysis and predefined levels or tolerance to find NECT slice thicknesses that allow for sufficiently accurate thrombus quantification. Results-: Thrombus length can be measured with high accuracy using the hyperdense middle cerebral artery sign detected in NECT images with slice thicknesses of 1.25 mm and 2.5 mm. We found mean deviations from the reference values and limits of agreement of-0.1 mm±0.6 mm with slice widths of 1.25 mm and 0.1 mm±0.7 mm for slice widths of 2.5 mm. Thrombus length measurements in NECT images with higher slice width and all evaluated thrombus volume measurements exhibited severe dependence on the level and did not match the accuracy criteria. Conclusion-: The length of the hyperdense middle cerebral artery sign as detected on thin-slice NECT reconstructions in patients with acute ischemic stroke can be used to quantify thrombotic burden accurately. Thus, it might qualify as a new diagnostic parameter in acute stroke management that indicates and quantifies the extent of vascular obliteration. {\textcopyright} 2010 American Heart Association, Inc.},
author = {Riedel, Christian H. and Jensen, Ulf and Rohr, Axel and Tietke, Marc and Alfke, Karsten and Ulmer, Stephan and Jansen, Olav},
doi = {10.1161/STROKEAHA.110.580662},
issn = {00392499},
journal = {Stroke},
keywords = {CT,acute care,acute stroke,embolic stroke,embolism,imaging,neuroradiology,stroke care,stroke management,thrombolysis},
number = {8},
pages = {1659--1664},
title = {{Assessment of thrombus in acute middle cerebral artery occlusion using thin-slice nonenhanced computed tomography reconstructions}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {41},
year = {2010}
}
@article{Rivest2009,
abstract = {Daily image guidance for helical tomotherapy prostate patients is based on the registration of pretreatment megavoltage CT (MVCT) images and the original planning CT. The goal of registration, whether manual or automatic, is the overlap of the prostate; otherwise prostate misplacement may compromise the efficacy of treatment or lead to increased toxicity. A previous study demonstrated that without the aid of implanted fiducials, manual registration results in inaccurate prostate positioning. The objective of this work is to quantify prostate misplacement that results from automatic bone matching (BM) and image matching (IM) registration algorithms. 204 MVCT images from eight high-risk tomotherapy prostate patients were incorporated into this retrospective study. BM and IM registration algorithms - based on maximization of mutual information of bony anatomy only and the entire image, respectively - were used to independently register MVCT images to their respective planning images. A correlation coefficient based algorithm that uses known planning CT contour information was used for automatic prostate localization in each MVCT image. Daily prostate misplacement was determined by repositioning as calculated from the BM and the IM algorithms. Mean (± SD) and maximum 3D prostate positioning errors were 3.7 ± 2.1 mm and 11.8 mm for bone matching, and 4.6 ± 2.3 mm and 11.5 mm for image matching. In terms of translational directions, IM would lead to prostate positioning error ≥ 3 mm in any of the LR, AP or SI directions in 62{\%} of treatment fractions. The corresponding value for BM is 51{\%}. The values for positioning errors ≥ 5 mm were 29{\%} and 17{\%} for IM and BM, respectively. This data suggests automatic daily image guidance for tomotherapy prostate patients should be based on bone matching instead of image matching.},
author = {Rivest, D. Ryan C. and Riauka, Terence A. and Murtha, Albert D. and Fallone, B. Gino},
doi = {10.1120/jacmp.v10i4.3071},
issn = {15269914},
journal = {Journal of Applied Clinical Medical Physics},
keywords = {Helical tomotherapy,Image registration,Prostate motion},
number = {4},
pages = {165--176},
title = {{Prostate positioning errors associated with two automatic registration based image guidance strategies}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {10},
year = {2009}
}
@article{Roach2009,
abstract = {Advances in systems biology and bioinformatics have highlighted that no cell population is truly uniform and that stochastic behavior is an inherent property of many biological systems. As a result, bulk measurements can be misleading even when particular care has been taken to isolate a single cell type, and measurements averaged over multiple cell populations in a tissue can be as misleading as the average height at an elementary school. There is a growing need for experimental techniques that can provide a combination of single cell resolution, large cell populations, and the ability to track cells over multiple time points. In this article, a microwell array cytometry platform was developed to meet this need and investigate the heterogeneity and stochasticity of cell behavior on a single cell basis. The platform consisted of a microfabricated device with high-density arrays of cell-sized microwells and custom software for automated image processing and data analysis. As a model experimental system, we used primary hepatocytes labeled with fluorescent probes sensitive to mitochondrial membrane potential and free radical generation. The cells were exposed to oxidative stress and the responses were dynamically monitored for each cell. The resulting data was then analyzed using bioinformatics techniques such as hierarchical and k-means clustering to visualize the data and identify interesting features. The results showed that clustering of the dynamic data not only enhanced comparisons between the treatment groups but also revealed a number of distinct response patterns within each treatment group. Heatmaps with hierarchical clustering also provided a data-rich complement to survival curves in a dose response experiment. The microwell array cytometry platform was shown to be powerful, easy to use, and able to provide a detailed picture of the heterogeneity present in cell responses to oxidative stress. We believe that our microwell array cytometry platform will have general utility for a wide range of questions related to cell population heterogeneity, biological stochasticity, and cell behavior under stress conditions. {\textcopyright} 2009 American Institute of Chemical Engineers.},
author = {Roach, Kenneth L. and King, Kevin R. and Uygun, Basak E. and Kohane, Isaac S. and Yarmush, Martin L. and Toner, Mehmet},
doi = {10.1002/btpr.289},
issn = {87567938},
journal = {Biotechnology Progress},
keywords = {Cytometry,Free radicals,Hepatocytes,Membrane potential,Microfabrication,Microwells,Mitochondria},
number = {6},
pages = {1772--1779},
title = {{High throughput single cell bioinformatics}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {25},
year = {2009}
}
@inproceedings{Rohn,
abstract = {Understanding complex biological systems requires data from manifold biological levels. Often this data is analysed in some meaningful context, for example, by integrating it into biological networks. However, spatial data given as 2D images or 3D volumes is commonly not taken into consideration and analysed separately. Here we present a new approach to integrate and analyse complex multimodal biological data in space and time. We present a data structure to manage this kind of data and discuss application examples for different data integration scenarios.},
author = {Rohn, Hendrik and Klukas, Christian and Schreiber, Falk},
booktitle = {GCB 2009 - German Conference on Bioinformatics 2009},
isbn = {9783885792512},
pages = {105--115},
title = {{Integration and visualisation of multimodal biological data}},
type = {Conference Proceedings},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79960202320{\&}partnerID=40{\&}md5=c0b665d0351eb138a112ad74c961d17d},
year = {2009}
}
@article{Rueden2017,
abstract = {Background: ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Results: We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called "ImageJ2" in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. Conclusions: Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ's development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.},
archivePrefix = {arXiv},
arxivId = {1701.05940},
author = {Rueden, Curtis T. and Schindelin, Johannes and Hiner, Mark C. and DeZonia, Barry E. and Walter, Alison E. and Arena, Ellen T. and Eliceiri, Kevin W.},
doi = {10.1186/s12859-017-1934-z},
eprint = {1701.05940},
issn = {14712105},
journal = {BMC Bioinformatics},
keywords = {Extensibility,Image processing,ImageJ,ImageJ2,Interoperability,N-dimensional,Open development,Open source,Reproducibility},
number = {1},
pages = {26},
title = {{ImageJ2: ImageJ for the next generation of scientific image data}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {18},
year = {2017}
}
@article{Rupp2006,
abstract = {Applications of computer vision and signal processing are often based on a set of basic and commonly accepted ideas and algorithms. Thus, when developing new approaches, reuse plays a decisive role. Unfortunately, scientists are rarely familiar with the powerful concepts that the software engineering community provides in order to develop reusable software nor do they have the appropriate experience to apply these existing techniques right. For this reason, we present fundamental design and implementation aspects of component-based software frameworks, which should help to develop component-based software frameworks for a given application field.},
author = {Rupp, Stephan and Daum, Volker},
issn = {11092750},
journal = {WSEAS Transactions on Computers},
keywords = {Plugin-based software framework,Reflexion mechanism,Software components},
number = {2},
pages = {425--432},
title = {{Design and implementation aspects for plugin-base software frameworks}},
type = {Journal Article},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33645140919{\&}partnerID=40{\&}md5=8bdab8bf2d3ec049f4709850ec61d0c4},
volume = {5},
year = {2006}
}
@article{Rusu2014,
abstract = {Purpose: In this work, the authors introduce a novel framework, the anatomically constrained registration (AnCoR) scheme and apply it to create a fused anatomic-disease atlas of the prostate which the authors refer to as the prostatome. The prostatome combines a MRI based anatomic and a histology based disease atlas. Statistical imaging atlases allow for the integration of information across multiple scales and imaging modalities into a single canonical representation, in turn enabling a fused anatomical-disease representation which may facilitate the characterization of disease appearance relative to anatomic structures. While statistical atlases have been extensively developed and studied for the brain, approaches that have attempted to combine pathology and imaging data for study of prostate pathology are not extant. This works seeks to address this gap. Methods: The AnCoR framework optimizes a scoring function composed of two surface (prostate and central gland) misalignment measures and one intensity-based similarity term. This ensures the correct mapping of anatomic regions into the atlas, even when regional MRI intensities are inconsistent or highly variable between subjects. The framework allows for creation of an anatomic imaging and a disease atlas, while enabling their fusion into the anatomic imaging-disease atlas. The atlas presented here was constructed using 83 subjects with biopsy confirmed cancer who had pre-operative MRI (collected at two institutions) followed by radical prostatectomy. The imaging atlas results from mapping thein vivo MRI into the canonical space, while the anatomic regions serve as domain constraints. Elastic co-registration MRI and corresponding ex vivo histology provides " ground truth" mapping of cancer extent on in vivo imaging for 23 subjects. Results: AnCoR was evaluated relative to alternative construction strategies that use either MRI intensities or the prostate surface alone for registration. The AnCoR framework yielded a central gland Dice similarity coefficient (DSC) of 90{\%}, and prostate DSC of 88{\%}, while the misalignment of the urethra and verumontanum was found to be 3.45 mm, and 4.73 mm, respectively, which were measured to be significantly smaller compared to the alternative strategies. As might have been anticipated from our limited cohort of biopsy confirmed cancers, the disease atlas showed that most of the tumor extent was limited to the peripheral zone. Moreover, central gland tumors were typically larger in size, possibly because they are only discernible at a much later stage. Conclusions: The authors presented the AnCoR framework to explicitly model anatomic constraints for the construction of a fused anatomic imaging-disease atlas. The framework was applied to constructing a preliminary version of an anatomic-disease atlas of the prostate, the prostatome. The prostatome could facilitate the quantitative characterization of gland morphology and imaging features of prostate cancer. These techniques, may be applied on a large sample size data set to create a fully developed prostatome that could serve as a spatial prior for targeted biopsies by urologists. Additionally, the AnCoR framework could allow for incorporation of complementary imaging and molecular data, thereby enabling their careful correlation for population based radio-omics studies. {\textcopyright} 2014 American Association of Physicists in Medicine.},
author = {Rusu, Mirabela and Bloch, B. Nicolas and Jaffe, Carl C. and Genega, Elizabeth M. and Lenkinski, Robert E. and Rofsky, Neil M. and Feleppa, Ernest and Madabhushi, Anant},
doi = {10.1118/1.4881515},
issn = {00942405},
journal = {Medical Physics},
keywords = {anatomic imaging atlas,guided biopsy,image processing,in vivo imaging,prostate cancer},
number = {7},
pages = {12},
title = {{Prostatome: A combined anatomical and disease based MRI atlas of the prostate}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {41},
year = {2014}
}
@article{Savolainen2013,
abstract = {Boron Neutron Capture Therapy (BNCT) is a binary radiotherapy method developed to treat patients with certain malignant tumours. To date, over 300 treatments have been carried out at the Finnish BNCT facility in various on-going and past clinical trials. In this technical review, we discuss our research work in the field of medical physics to form the groundwork for the Finnish BNCT patient treatments, as well as the possibilities to further develop and optimize the method in the future. Accordingly, the following aspects are described: neutron sources, beam dosimetry, treatment planning, boron imaging and determination, and finally the possibilities to detect the efficacy and effects of BNCT on patients. {\textcopyright} 2012 Associazione Italiana di Fisica Medica.},
author = {Savolainen, Sauli and Kortesniemi, Mika and Timonen, Marjut and Reijonen, Vappu and Kuusela, Linda and Uusi-Simola, Jouni and Salli, Eero and Koivunoro, Hanna and Sepp{\"{a}}l{\"{a}}, Tiina and L{\"{o}}nnroth, Nadja and V{\"{a}}lim{\"{a}}ki, Petteri and Hyv{\"{o}}nen, Heini and Kotiluoto, Petri and Ser{\'{e}}n, Tom and Kuronen, Antti and Heikkinen, Sami and Kosunen, Antti and Auterinen, Iiro},
doi = {10.1016/j.ejmp.2012.04.008},
issn = {11201797},
journal = {Physica Medica},
keywords = {Beam dosimetry,Boron imaging and determination,Diffusion imaging,Dose calculation,Image registration,Neutron dosimetry,Neutron sources,Treatment planning},
number = {3},
pages = {233--248},
title = {{Boron neutron capture therapy (BNCT) in Finland: Technological and physical prospects after 20 years of experiences}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {29},
year = {2013}
}
@inbook{Scheenstra2007,
abstract = {In biological image processing the segmentation of a volume is, although tedious, required for many applications, like the comparison of structures and annotation purposes. To automate this process, we present a segmentation method for various structures of the mouse brain. The segmentation consists of two parts; first a rough affine atlas-based registration was performed and second, the edges between structures were refined by an adapted Markov random field clustering approach. The segmentations results were compared to manual segmentations from two experts. The presented automatic segmentation method is quick, intuitive and suitable for registration purposes, but also for biological objectives, like comparison and annotation.},
address = {Bellingham},
author = {Scheenstra, Alize E. H. and Dijkstra, Jouke and van de Ven, Rob C. G. and van der Weerd, Louise and Reiber, Johan H. C.},
booktitle = {Medical Imaging 2007: Physiology, Function, and Structure from Medical Images},
doi = {10.1117/12.708867},
editor = {Manduca, A and Hu, X P},
isbn = {0819466298},
issn = {16057422},
pages = {651106},
publisher = {Spie-Int Soc Optical Engineering},
series = {Proceedings of SPIE},
title = {{Automated segmentation of the ex vivo mouse brain}},
type = {Book Section},
url = {{\%}3CGo to},
volume = {6511},
year = {2007}
}
@incollection{Scheenstra2009,
abstract = {Non-rigid registration of MR images to a common reference image results in deformation fields, from which anatomical differences can be statistically assessed, within and between populations. Without further assumptions, nonparametric tests are required and currently the analysis of deformation fields is performed by permutation tests. For deformation fields, often the vector magnitude is chosen as test statistic, resulting in a loss of information. In this paper, we consider the three dimensional Moore-Rayleigh test as an alternative for permutation tests. This nonparametric test offers two novel features: first, it incorporates both the directions and magnitude of the deformation vectors. Second, as its distribution function is available in closed form, this test statistic can be used in a clinical setting. Using synthetic data that represents variations as commonly encountered in clinical data, we show that the Moore-Rayleigh test outperforms the classical permutation test. {\textcopyright} 2009 Springer Berlin Heidelberg.},
author = {Scheenstra, Alize E.H. and Muskulus, Michael and Staring, Marius and {Van Den Maagdenberg}, Arn M.J.V. and {Verduyn Lunel}, Sjoerd and Reiber, J. Hans C. and {Van Der Weerd}, Louise and Dijkstra, Jouke},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
doi = {10.1007/978-3-642-02498-6_47},
isbn = {3642024971},
issn = {03029743},
pages = {564--575},
title = {{The 3D moore-rayleigh test for the quantitative groupwise comparison of MR brain images}},
type = {Serial},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-70349313285{\&}doi=10.1007{\%}2F978-3-642-02498-6{\_}47{\&}partnerID=40{\&}md5=6667d3c02eda486716d2cfb5e09e139d},
volume = {5636 LNCS},
year = {2009}
}
@article{Scheenstra2009a,
abstract = {Segmentation of magnetic resonance imaging (MRI) data is required for many applications, such as the comparison of different structures or time points, and for annotation purposes. Currently, the gold standard for automated image segmentation is nonlinear atlas-based segmentation. However, these methods are either not sufficient or highly time consuming for mouse brains, owing to the low signal to noise ratio and low contrast between structures compared with other applications. We present a novel generic approach to reduce processing time for segmentation of various structures of mouse brains, in vivo and ex vivo. The segmentation consists of a rough affine registration to a template followed by a clustering approach to refine the rough segmentation near the edges. Compared with manual segmentations, the presented segmentation method has an average kappa index of 0.7 for 7 of 12 structures in in vivo MRI and 11 of 12 structures in ex vivo MRI. Furthermore, we found that these results were equal to the performance of a nonlinear segmentation method, but with the advantage of being 8 times faster. The presented automatic segmentation method is quick and intuitive and can be used for image registration, volume quantification of structures, and annotation. {\textcopyright} 2009 BC Decker Inc.},
author = {Dijkstra, Jouke and Scheenstra, Alize E.H. and {Van De Ven}, Rob C.G. and {Van Weerd}, Louise Der and {Van Den Maagdenberg}, Arn M.J.M. and Reiber, Johan H.C.},
doi = {10.2310/7290.2009.00004},
issn = {15353508},
journal = {Molecular Imaging},
number = {1},
pages = {35--44},
title = {{Automated segmentation of in vivo and ex vivo mouse brain magnetic resonance images}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {8},
year = {2009}
}
@article{Schindelin2015,
abstract = {Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem.},
author = {Schindelin, Johannes and Rueden, Curtis T. and Hiner, Mark C. and Eliceiri, Kevin W.},
doi = {10.1002/mrd.22489},
issn = {10982795},
journal = {Molecular Reproduction and Development},
number = {7-8},
pages = {518--529},
title = {{The ImageJ ecosystem: An open platform for biomedical image analysis}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {82},
year = {2015}
}
@article{Schmitz2017,
abstract = {Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50{\%} and 75{\%} of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10 5 to 1 × 10 6 cells/mm 3. Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.},
author = {Schmitz, Alexander and Fischer, Sabine C. and Mattheyer, Christian and Pampaloni, Francesco and Stelzer, Ernst H.K.},
doi = {10.1038/srep43693},
issn = {20452322},
journal = {Scientific Reports},
pages = {13},
title = {{Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {7},
year = {2017}
}
@article{Schmitz2018,
abstract = {3D-Polarized Light Imaging (3D-PLI) enables high-resolution three-dimensional mapping of the nerve fiber architecture in unstained histological brain sections based on the intrinsic birefringence of myelinated nerve fibers. The interpretation of the measured birefringent signals comes with conjointly measured information about the local fiber birefringence strength and the fiber orientation. In this study, we present a novel approach to disentangle both parameters from each other based on a weighted least squares routine (ROFL) applied to oblique polarimetric 3D-PLI measurements. This approach was compared to a previously described analytical method on simulated and experimental data obtained from a post mortem human brain. Analysis of the simulations revealed in case of ROFL a distinctly increased level of confidence to determine steep and flat fiber orientations with respect to the brain sectioning plane. Based on analysis of histological sections of a human brain dataset, it was demonstrated that ROFL provides a coherent characterization of cortical, subcortical, and white matter regions in terms of fiber orientation and birefringence strength, within and across sections. Oblique measurements combined with ROFL analysis opens up new ways to determine physical brain tissue properties by means of 3D-PLI microscopy.},
author = {Schmitz, Daniel and Muenzing, Sascha E.A. and Schober, Martin and Schubert, Nicole and Minnerop, Martina and Lippert, Thomas and Amunts, Katrin and Axer, Markus},
doi = {10.3389/fnana.2018.00075},
issn = {16625129},
journal = {Frontiers in Neuroanatomy},
keywords = {3D-PLI,Fiber architecture,Modeling,Neuroimaging,White matter anatomy},
pages = {15},
title = {{Derivation of Fiber Orientations From Oblique Views Through Human Brain Sections in 3D-Polarized Light Imaging}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {12},
year = {2018}
}
@inproceedings{Schreiber,
abstract = {This article describes a method for the automatic detection of the proximal femur in radiographs using a template-based mutual information registration method. It will be part of a planned, larger system for automated estimation of osteoporosis in the femoral neck. Our multi-step optimization process achieves a successful registration rate of 70{\%} to 95{\%}.},
author = {Schreiber, Jan and Schubert, Rainer and Kuhn, Volker},
booktitle = {Informatik aktuell},
doi = {10.1007/3-540-32137-3_23},
isbn = {9783540321361},
issn = {1431472X},
pages = {111--115},
title = {{Femur detection in radiographs using template-based registration}},
type = {Conference Proceedings},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77949583057{\&}partnerID=40{\&}md5=71c5eb7ea5d62e5a2e9b0450a8d52b56},
year = {2006}
}
@incollection{Shah2014,
abstract = {Although variousmodalities are used in prostate cancer imaging, transrectal ultrasound (TRUS) guided biopsy remains the gold standard for diagnosis. However, TRUS suffers from low sensitivity, leading to an elevated rate of false negative results. Magnetic Resonance Imaging (MRI) on the other hand provides currently the most accurate imagebased evaluation of the prostate. Thus, TRUS/MRI fusion image-guided biopsy has evolved to be the method of choice to circumvent the limitations of TRUS-only biopsy. Most commercial frameworks that offer such a solution rely on rigid TRUS/MRI fusion and rarely use additional information from other modalities such as Positron Emission Tomography (PET). Other frameworks require long interaction times and are complex to integrate with the clinical workflow. Available solutions are not fully able to meet the clinical requirements of speed and high precision at low cost simultaneously.We introduce an open source fusion biopsy framework that is low cost, simple to use and has minimal overhead in clinical workflow. Hence, it is ideal as a research platform for the implementation and rapid bench to bedside translation of new image registration and visualization approaches. We present the current status of the framework that uses pre-interventional PET and MRI rigidly registered with 3D TRUS for prostate biopsy guidance and discuss results from first clinical cases.},
author = {Shah, Amit and Zettinig, Oliver and Maurer, Tobias and Precup, Cristina and {Schulte Zu Berge}, Christian and Weiss, Jakob and Frisch, Benjamin and Navab, Nassir},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
doi = {10.1007/978-3-319-13909-8_1},
issn = {16113349},
keywords = {MRI,Multimodal image-guided biopsy,Open source software,PET,Prostate cancer,TRUS},
title = {{An Open Source Multimodal Image-Guided Prostate Biopsy Framework}},
type = {Serial},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84921489612{\&}doi=10.1007{\%}2F978-3-319-13909-8{\_}1{\&}partnerID=40{\&}md5=dda55817f88614188e848aa38b528c3b},
volume = {8680},
year = {2014}
}
@inproceedings{Shah,
abstract = {Studies have shown that vascular structure of a solitary pulmonary nodule (SPN) can give insight into the diagnosis of the nodule. The purpose of this study is to investigate the utility of texture analysis as a quantitative measure of the vascular structure of a nodule. A contrast CT study was conducted for 29 patients with an indeterminate SPN. For each patient, the post-contrast series at maximum enhancement was volumetrically registered to the pre-contrast series. The two registered series were subtracted to form difference images of the nodule and each voxel was color-coded into 7 bins. Initially, a representative image of each nodule was subjectively rated on a five-point by a radiologist as to the magnitude, extent, and heterogeneity of the enhancement. From the initial analysis the heterogeneity of the nodule was found to be significantly different for benign versus malignant nodules (p{\textless}0.01), while the other two ratings were found not to be significant. We then attempted to quantify this subjective rating of heterogeneity by calculating 14 textural features based on co-occurrence matrices. These features included various measures of contrast, entropy, energy, etc. Dimension reduction techniques such as principal component and factor analysis were applied to the features to reduce the 14 variables to one factor. The mean of this factor was significantly different for malignant versus benign nodules (p=0.010). Texture analysis of contrast enhancement maps appears to be useful tool to characterize SPNs.},
author = {Shah, Sumit K. and McNitt-Gray, Michael F. and Petkovska, Iva and Kim, Hyun Jun and DeZoysa, Kheshini R. and Goldin, Jonathan G. and Suh, Robert D. and Aberle, Denise R.},
booktitle = {Medical Imaging 2005: Image Processing},
doi = {10.1117/12.595874},
issn = {16057422},
pages = {1950},
title = {{Solitary pulmonary nodule characterization on CT by use of contrast enhancement maps}},
type = {Conference Proceedings},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-23844470662{\&}doi=10.1117{\%}2F12.595874{\&}partnerID=40{\&}md5=cb9ec8d5c13ffb11b3fdaa3d4b5bb75d},
volume = {5747},
year = {2005}
}
@article{Shams2018,
abstract = {Image guidance has become the standard of care for patient positioning in radiotherapy, where image registration is often a critical step to help manage patient motion. However, in practice, verification of registration quality is often adversely affected by difficulty in manual inspection of 3-D images and time constraint, thus affecting the therapeutic outcome. Therefore, we proposed to employ both bootstrapping and the supervised learning methods of linear discriminant analysis and random forest to help robustly assess registration quality in ultrasound-guided radiotherapy. We validated both approaches using phantom and real clinical ultrasound images, and showed that both performed well for the task. While learning-based techniques offer better accuracy and shorter evaluation time, bootstrapping requires no prior training and has a higher sensitivity.},
author = {Shams, Roozbeh and Xiao, Yiming and Hebert, Francois and Abramowitz, Matthew and Brooks, Rupert and Rivaz, Hassan},
doi = {10.1109/TMI.2017.2755695},
issn = {1558254X},
journal = {IEEE Transactions on Medical Imaging},
keywords = {Radiotherapy,bootstrapping,image registration,motion management,quality management,supervised learning},
number = {2},
pages = {428--437},
title = {{Assessment of Rigid Registration Quality Measures in Ultrasound-Guided Radiotherapy}},
type = {Journal Article},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85030780937{\&}doi=10.1109{\%}2FTMI.2017.2755695{\&}partnerID=40{\&}md5=c0b386f770628888db0e4e521b9905ba},
volume = {37},
year = {2018}
}
@article{Shao2014,
abstract = {Intensity-based 2D/3D registration is a key technique using digitally reconstructed radiographs (DRRs) to register the preoperative volume to the patient setup during the operation. Although DRR-based method provides a high accuracy, the small capture range hinders its clinical use. In this paper, such problem was addressed by a robust and fast initialization method using a two-level scheme including automatic tracking-based initialization (Level I) and multiresolution estimation based on central-slice theorem and phase correlation (Level II). It provided almost optimal transformation parameters for intensity-based registration. Experiments using a public gold standard data set and a spinal phantom have been conducted. The mean target registration error (mTRE) was limited in the range from 2.12 mm to 22.57 mm after tracking-based initialization. The capture range based on level II only was 20.1 mm and the mTRE in this capture range was 2.92 ± 2.21 mm. The intensity-based 2D/3D registration using proposed two-level initialization achieved the successful rate of 84.8{\%} with the average error of 2.36 mm. The experimental results showed that the proposed method yielded the robust and fast initialization for intensity-based registration methods. In a similar way, it can be applied to other registration methods to enable a larger capture range and robust implementation. {\textcopyright} 2014 Zhenzhou Shao et al.},
author = {Shao, Zhenzhou and Han, Jianda and Liang, Wei and Tan, Jindong and Guan, Yong},
doi = {10.1155/2014/989254},
issn = {16878140},
journal = {Advances in Mechanical Engineering},
pages = {12},
title = {{Robust and fast initialization for intensity-based 2D/3D registration}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {2014},
year = {2014}
}
@inproceedings{Shen,
abstract = {This paper describes the Medical Visualizer, a real-time visualization system for analyzing medical volumetric data in various virtual environments, such as autostereoscopic displays, dual-projector screens and immersive environments such as the CAVE. Direct volume rendering is used for visualizing the details of medical volumetric data sets without intermediate geometric representations. By interactively manipulating the color and transparency functions through the friendly user interface, radiologists can either inspect the data set as a whole or focus on a specific region. In our system, 3D texture hardware is employed to accelerate the rendering process. The system is designed to be platform independent, as all virtual reality functions are separated from kernel functions. Due to its modular design, our system can be easily extended to other virtual environments, and new functions can be incorporated rapidly. {\textcopyright} 2008 IEEE.},
author = {Shen, Rui and Boulanger, Pierre and Noga, Michelle},
booktitle = {Proceedings - 5th International Conference BioMedical Visualization, Information Visualization in Medical and Biomedical Informatics, MediVis 2008},
doi = {10.1109/MediVis.2008.10},
isbn = {9780769532844},
pages = {63--70},
title = {{Med vis: A real-time immersive visualization environment for the exploration of medical volumetric data}},
type = {Conference Proceedings},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-57849137509{\&}doi=10.1109{\%}2FMediVis.2008.10{\&}partnerID=40{\&}md5=11410f98c18a5d2bb0c6538a8af8ee5e},
year = {2008}
}
@inproceedings{Shena,
abstract = {Nowadays, the effective utilization of open-source software could significantly boost both clinical research and practices, especially in resource-poor countries. However, the plethora of open-source clinical software has left many people unable to quickly locate the appropriate one for their needs. Commonly available software quality metrics and software documentation, such as downloads, forks, stars, and readme files, are useful selection criteria, but they only indicate the software quality from the perspective of IT experts. This paper proposes a method that offers additional insights on the performance and effectiveness of clinical software. It links open-source clinical software with relevant scientific literature, such as papers that use case studies of clinical software to reveal the strength and weakness of a given software from the clinical perspective. To interactively present the open-source clinical software and their related literature, we have developed the LOCATE web application that enables users to explore related literature for a given opensource clinical software. Moreover, the peer-review cycle of the application allows users to improve the application by confirming, adding or removing related literature. An evaluation experiment of the five most popular open-source clinical tools demonstrates the potential usefulness of LOCATE.},
author = {Shen, Zhengru and Spruit, Marco},
booktitle = {HEALTHINF 2019 - 12th International Conference on Health Informatics, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019},
doi = {10.5220/0007378702940301},
isbn = {9789897583537},
keywords = {Github Repository,Literature,Open-source Clinical Software,Web Application},
pages = {294--301},
title = {{LOCATE: A web application to link open-source clinical software with literature}},
type = {Conference Proceedings},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064637892{\&}partnerID=40{\&}md5=e5fa660669c558180b42f873a3ef3683},
year = {2019}
}
@article{Sjoberg2013,
abstract = {Label fusion multi-atlas approaches for image segmentation can give better segmentation results than single atlas methods. We present a multi-atlas label fusion strategy based on probabilistic weighting of distance maps. Relationships between image similarities and segmentation similarities are estimated in a learning phase and used to derive fusion weights that are proportional to the probability for each atlas to improve the segmentation result. The method was tested using a leave-one-out strategy on a database of 21 pre-segmented prostate patients for different image registrations combined with different image similarity scorings. The probabilistic weighting yields results that are equal or better compared to both fusion with equal weights and results using the STAPLE algorithm. Results from the experiments demonstrate that label fusion by weighted distance maps is feasible, and that probabilistic weighted fusion improves segmentation quality more the stronger the individual atlas segmentation quality depends on the corresponding registered image similarity. The regions used for evaluation of the image similarity measures were found to be more important than the choice of similarity measure. {\textcopyright} 2013 Elsevier Ireland Ltd.},
author = {Sj{\"{o}}berg, C. and Ahnesj{\"{o}}, A.},
doi = {10.1016/j.cmpb.2012.12.006},
issn = {01692607},
journal = {Computer Methods and Programs in Biomedicine},
keywords = {Atlas based segmentation,Deformable registration,Label fusion,Multi-atlas segmentation,Radiotherapy prostate,Segmentation},
number = {3},
pages = {308--319},
title = {{Multi-atlas based segmentation using probabilistic label fusion with adaptive weighting of image similarity measures}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {110},
year = {2013}
}
@article{Song2020,
abstract = {To overcome the mechanical drawback of bioink, we proposed a supporter model to enhance the mechanical strength of bioprinted 3D constructs, in which a unit-assembly idea was involved. Based on Computed Tomography images of critical-sized rabbit bone defect, the 3D re-construction was accomplished by a sequenced process using Mimics 17.0, BioCAM and BioCAD software. 3D constructs were bioprinted using polycaprolactone (PCL) ink for the outer supporter under extrusion mode, and cell-laden tricalcium phosphate (TCP)/alginate bioink for the inner filler under air pressure dispensing mode. The relationship of viscosity of bioinks, 3D bioprinting pressure, TCP/alginate ratio and cell survival were investigated by the shear viscosities analysis, live/dead cell test and cell-counting kit 8 measurement. The viscosity of bioinks at 1.0 s−1-shear rate could be adjusted within the range of 1.75 ± 0.29 Pa{\textperiodcentered}s to 155.65 ± 10.86 Pa{\textperiodcentered}s by changing alginate concentration, corresponding to 10 kPa–130 kPa of printing pressure. This design with PCL supporter could significantly enhance the compressive strength and compressive modulus of standardized 3D mechanical testing specimens up to 2.15 ± 0.14 MPa to 2.58 ± 0.09 MPa, and 42.83 ± 4.75 MPa to 53.12 ± 1.19 MPa, respectively. Cells could maintain the high viability (over 80{\%}) under the given printing pressure but cell viability declined with the increase of TCP content. Cell survival after experiencing 7 days of cell culture could be achieved when the ratio of TCP/alginate was 1 : 4. All data supported the feasibility of the supporter and unit-assembly model to enhance mechanical properties of bioprinted 3D constructs.},
author = {Song, Jie Liang and Fu, Xin Ye and Raza, Ali and Shen, Nai An and Xue, Ya Qi and Wang, Hua Jie and Wang, Jin Ye},
doi = {10.1016/j.jmbbm.2019.103533},
issn = {18780180},
journal = {Journal of the Mechanical Behavior of Biomedical Materials},
keywords = {Alginate-TCP bioink,Bioprinting,Bone defect,PCL supporter,Unit-assembly model},
title = {{Enhancement of mechanical strength of TCP-alginate based bioprinted constructs}},
type = {Journal Article},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074942779{\&}doi=10.1016{\%}2Fj.jmbbm.2019.103533{\&}partnerID=40{\&}md5=5a9d1f1c5ade6a354c2e6bf7adb9613f},
volume = {103},
year = {2020}
}
@article{Song2009,
abstract = {Objective: To establish a virtual surgery system based on three-dimensional visualization technique which can help the doctors to plot the surgery. Methods: A curve was created on the 3D space, and some points added on the curve adjusted by controlling the points which could be added and deleted. The angle could be computed according to the final curves, thus to place the scalpel to give convenience to the real surgery. Results: The virtual surgery system was used in hospital, and the results were satisfied. Conclusion: The virtual surgery system added to medical image process system is helpful to decrease risk of surgical operation.},
author = {Song, Li Mei and Luo, Jing and Wen, Yu Hua},
issn = {10033289},
journal = {Chinese Journal of Medical Imaging Technology},
keywords = {Image process,Virtual segmentation,Virtual surgery,Visualization},
number = {8},
pages = {1481--1484},
title = {{Virtual surgery based on medical images}},
type = {Journal Article},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78650586605{\&}partnerID=40{\&}md5=047142ba89c1419e7f5474c726cfdc20},
volume = {25},
year = {2009}
}
@book{Song2009a,
abstract = {Objective: To establish a virtual surgery system based on three-dimensional visualization technique which can help the doctors to plot the surgery. Methods: A curve was created on the 3D space, and some points added on the curve adjusted by controlling the points which could be added and deleted. The angle could be computed according to the final curves, thus to place the scalpel to give convenience to the real surgery. Results: The virtual surgery system was used in hospital, and the results were satisfied. Conclusion: The virtual surgery system added to medical image process system is helpful to decrease risk of surgical operation.},
address = {New York},
author = {Song, Li Mei and Luo, Jing and Wen, Yu Hua},
booktitle = {Chinese Journal of Medical Imaging Technology},
isbn = {978-1-4244-2901-1},
issn = {10033289},
keywords = {Image process,Virtual segmentation,Virtual surgery,Visualization},
number = {8},
pages = {1481--1484},
publisher = {Ieee},
series = {2009 3rd International Conference on Bioinformatics and Biomedical Engineering, Vols 1-11},
title = {{Virtual surgery based on medical images}},
type = {Book},
url = {{\%}3CGo to},
volume = {25},
year = {2009}
}
@article{Soomro2019,
abstract = {The main goal of this work is to automatically segment colorectal tumors in 3D T2-weighted (T2w) MRI with reasonable accuracy. For such a purpose, a novel deep learning-based algorithm suited for volumetric colorectal tumor segmentation is proposed. The proposed CNN architecture, based on densely connected neural network, contains multiscale dense interconnectivity between layers of fine and coarse scales, thus leveraging multiscale contextual information in the network to get better flow of information throughout the network. Additionally, the 3D level-set algorithm was incorporated as a postprocessing task to refine contours of the network predicted segmentation. The method was assessed on T2-weighted 3D MRI of 43 patients diagnosed with locally advanced colorectal tumor (cT3/T4). Cross validation was performed in 100 rounds by partitioning the dataset into 30 volumes for training and 13 for testing. Three performance metrics were computed to assess the similarity between predicted segmentation and the ground truth (i.e., manual segmentation by an expert radiologist/oncologist), including Dice similarity coefficient (DSC), recall rate (RR), and average surface distance (ASD). The above performance metrics were computed in terms of mean and standard deviation (mean ± standard deviation). The DSC, RR, and ASD were 0.8406 ± 0.0191, 0.8513 ± 0.0201, and 2.6407 ± 2.7975 before postprocessing, and these performance metrics became 0.8585 ± 0.0184, 0.8719 ± 0.0195, and 2.5401 ± 2.402 after postprocessing, respectively. We compared our proposed method to other existing volumetric medical image segmentation baseline methods (particularly 3D U-net and DenseVoxNet) in our segmentation tasks. The experimental results reveal that the proposed method has achieved better performance in colorectal tumor segmentation in volumetric MRI than the other baseline techniques.},
author = {Soomro, Mumtaz Hussain and Coppotelli, Matteo and Conforto, Silvia and Schmid, Maurizio and Giunta, Gaetano and {Del Secco}, Lorenzo and Neri, Emanuele and Caruso, Damiano and Rengo, Marco and Laghi, Andrea},
doi = {10.1155/2019/1075434},
issn = {20402309},
journal = {Journal of Healthcare Engineering},
pages = {11},
title = {{Automated segmentation of colorectal tumor in 3D MRI Using 3D multiscale densely connected convolutional neural network}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {2019},
year = {2019}
}
@article{Soudah2017,
abstract = {In the last few years, wall shear stress (WSS) has arisen as a new diagnostic indicator in patients with arterial disease. There is a substantial evidence that the WSS plays a significant role, together with hemodynamic indicators, in initiation and progression of the vascular diseases. Estimation of WSS values, therefore, may be of clinical significance and the methods employed for its measurement are crucial for clinical community. Recently, four-dimensional (4D) flow cardiovascular magnetic resonance (CMR) has been widely used in a number of applications for visualization and quantification of blood flow, and although the sensitivity to blood flow measurement has increased, it is not yet able to provide an accurate three-dimensional (3D) WSS distribution. The aim of this work is to evaluate the aortic blood flow features and the associated WSS by the combination of 4D flow cardiovascular magnetic resonance (4D CMR) and computational fluid dynamics technique. In particular, in this work, we used the 4D CMR to obtain the spatial domain and the boundary conditions needed to estimate the WSS within the entire thoracic aorta using computational fluid dynamics. Similar WSS distributions were found for cases simulated. A sensitivity analysis was done to check the accuracy of the method. 4D CMR begins to be a reliable tool to estimate the WSS within the entire thoracic aorta using computational fluid dynamics. The combination of both techniques may provide the ideal tool to help tackle these and other problems related to wall shear estimation.},
author = {Soudah, E. and Casacuberta, J. and Gamez-Montero, P. J. and P{\'{e}}rez, J. S. and Rodr{\'{i}}guez-Cancio, M. and Raush, G. and Li, C. H. and Carreras, F. and Castilla, R.},
doi = {10.1142/S0219519417500464},
issn = {02195194},
journal = {Journal of Mechanics in Medicine and Biology},
keywords = {Phase-contrast MRI,blood flow patterns,computational fluid dynamics,velocity mapping,wall shear stress},
number = {3},
pages = {16},
title = {{Estimation of wall shear stress using 4D flow cardiovascular MRI and computational fluid dynamics}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {17},
year = {2017}
}
@article{Spadea2014,
abstract = {Methods and Materials: Six lung cancer patients CT scans were preprocessed by masking out the gross tumor volume (GTV), and digitally reconstructed radiographs along the planned beams eye view (BEV) were generated, for a total of 27 projections. Proton radiographies (PR) were also computed for the same BEV through Monte Carlo simulations. The digitally reconstructed radiograph was subtracted from the corresponding proton image, resulting in a contrast-enhanced proton radiography (CEPR). Michelson contrast analysis was performed both on PR and CEPR. The tumor region was then automatically segmented on CEPR and compared to the ground truth (GT) provided by physicians in terms of Dice coefficient, accuracy, precision, sensitivity, and specificity.
Purpose: To obtain a contrasted image of the tumor region during the setup for proton therapy in lung patients, by using proton radiography and x-ray computed tomography (CT) prior knowledge.
Results: Contrast on CEPR was, on average, 4 times better than on PR. For 10 lateral projections (±45 off of 90 or 270), although it was not possible to distinguish the tumor region in the PR, CEPR offers excellent GTV visibility. The median ± quartile values of Dice, precision, and accuracy indexes were 0.86 ± 0.03, 0.86 ± 0.06, and 0.88 ± 0.02, respectively, thus confirming the reliability of the method in highlighting tumor boundaries. Sensitivity and specificity analysis demonstrated that there is no systematic over- or underestimation of the tumor region. Identification of the tumor boundaries using CEPR resulted in a more accurate and precise definition of GTV compared to that obtained from pretreatment CT.
Conclusions: In most proton centers, the current clinical protocol is to align the patient using kV imaging with bony anatomy as a reference. We demonstrated that CEPR can significantly improve tumor visualization, allowing better patient set-up and permitting image guided proton therapy (IGPT).},
author = {Spadea, Maria Francesca and Fassi, Aurora and Zaffino, Paolo and Riboldi, Marco and Baroni, Guido and Depauw, Nicolas and Seco, Joao},
doi = {10.1016/j.ijrobp.2014.06.057},
issn = {1879355X},
journal = {International Journal of Radiation Oncology Biology Physics},
number = {3},
pages = {628--636},
title = {{Contrast-enhanced proton radiography for patient set-up by using x-ray CT prior knowledge}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {90},
year = {2014}
}
@article{Spanakis2019,
abstract = {Evolutionary algorithms have been used recently as an alternative in image registration, especially in cases where the similarity function is non-convex with many local optima. However, their drawback is that they tend to be computationally expensive. Trying to avoid local minima can increase the computational cost. The purpose of authors' research is to minimise the duration of the image registration process. This paper presents a method to minimise the computational cost by introducing a machine learning-based variant of Harmony Search. To this end, a series of machine-learning regression methods are tested in order to find the most appropriate that minimises the cost without degrading the quality of the results. The best regression method is then incorporated in the optimisation process and is compared with two well-known ITK image registration methods. The comparison of authors' image registration method with ITK concerns both the quality of the results and the duration of the registration experiments. The comparison is done on a set of random image pairs of various sources (e.g. medical or satellite images), and the encouraging results strongly indicate that authors' method can be used in a variety of image registration applications producing quality results in significantly less time.},
author = {Spanakis, Constantinos and Mathioudakis, Emmanouil and Kampanis, Nikos and Tsiknakis, Manolis and Marias, Kostas},
doi = {10.1049/iet-ipr.2018.5389},
issn = {17519659},
journal = {IET Image Processing},
number = {5},
pages = {843--849},
title = {{Machine-learning regression in evolutionary algorithms and image registration}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {13},
year = {2019}
}
@article{Sparks2015,
abstract = {Purpose: Transrectal ultrasound (TRUS)-guided needle biopsy is the current gold standard for prostate cancer diagnosis. However, up to 40{\%} of prostate cancer lesions appears isoechoic on TRUS. Hence, TRUS-guided biopsy has a high false negative rate for prostate cancer diagnosis. Magnetic resonance imaging (MRI) is better able to distinguish prostate cancer from benign tissue. However, MRI-guided biopsy requires special equipment and training and a longer procedure time. MRI-TRUS fusion, where MRI is acquired preoperatively and then aligned to TRUS, allows for advantages of both modalities to be leveraged during biopsy. MRI-TRUS-guided biopsy increases the yield of cancer positive biopsies. In this work, the authors present multiattribute probabilistic postate elastic registration (MAPPER) to align prostate MRI and TRUS imagery. Methods: MAPPER involves (1) segmenting the prostate on MRI, (2) calculating a multiattribute probabilistic map of prostate location on TRUS, and (3) maximizing overlap between the prostate segmentation on MRI and the multiattribute probabilistic map on TRUS, thereby driving registration of MRI onto TRUS. MAPPER represents a significant advancement over the current state-of-the-art as it requires no user interaction during the biopsy procedure by leveraging texture and spatial information to determine the prostate location on TRUS. Although MAPPER requires manual interaction to segment the prostate on MRI, this step is performed prior to biopsy and will not substantially increase biopsy procedure time. Results: MAPPER was evaluated on 13 patient studies from two independent datasetsDataset 1 has 6 studies acquired with a side-firing TRUS probe and a 1.5 T pelvic phased-array coil MRI; Dataset 2 has 7 studies acquired with a volumetric end-firing TRUS probe and a 3.0 T endorectal coil MRI. MAPPER has a root-mean-square error (RMSE) for expert selected fiducials of 3.36±1.10 mm for Dataset 1 and 3.14±0.75 mm for Dataset 2. State-of-the-art MRI-TRUS fusion methods report RMSE of 3.062.07 mm. Conclusions: MAPPER aligns MRI and TRUS imagery without manual intervention ensuring efficient, reproducible registration. MAPPER has a similar RMSE to state-of-the-art methods that require manual intervention.},
author = {Sparks, Rachel and {Nicolas Bloch}, B. and Feleppa, Ernest and Barratt, Dean and Moses, Daniel and Ponsky, Lee and Madabhushi, Anant},
doi = {10.1118/1.4905104},
issn = {00942405},
journal = {Medical Physics},
keywords = {MRI-ultrasound fusion,image registration,image-guided biopsy,prostate cancer,prostate imaging},
number = {3},
pages = {1153--1163},
title = {{Multiattribute probabilistic prostate elastic registration (MAPPER): Application to fusion of ultrasound and magnetic resonance imaging}},
type = {Journal Article},
url = {{\%}3CGo to},
volume = {42},
year = {2015}
}
@article{Srinivasan2018,
abstract = {Purpose: In this study, a 3D fat-based deformable registration algorithm was developed for registering dynamic contrast-enhanced breast images. Methods: The mutual information similarity measure

license_type: permissive

branch_name: refs/heads/master

extension: bib