@article {2470,
	title = {Data-driven characterization of knee structures using non-negative matrix factorization of 3D multi-echo UTE MRI},
	journal = {NMR in Biomedicine},
	year = {In Press},
	author = {C{\'e}line Smekens and Pieter Van Dyck and Patrick S Fuchs and Jan Sijbers and Thomas Janssens and Ben Jeurissen}
}
@inproceedings {2442,
	title = {Cycloidal Acquisition for Inline Edge Illumination X-ray Phase Contrast Computed Tomography: A Simulation Study},
	booktitle = {15th Conference on Industrial Computed Tomography (iCT)},
	volume = {31},
	year = {2026},
	month = {February},
	address = {Linz, Austria},
	keywords = {computed tomography, edge illumination, inline acquisition, X-ray phase contrast imaging},
	doi = {10.58286/32604},
	url = {https://doi.org/10.58286/32604},
	author = {Verstraete, J. and Francken, N. and Jan Sijbers and Jan De Beenhouwer}
}
@inproceedings {2443,
	title = {Inline Edge Illumination Computed Tomography: A Simulation Study},
	booktitle = {2026 IEEE 23rd Mediterranean Electrotechnical Conference (MELECON)},
	year = {2026},
	address = {Cairo, Egypt},
	keywords = {edge illumination, Industry 4.0, Inline inspection, Non-destructive testing, X-ray phase contrast computed tomography},
	doi = {https://doi.org/10.1109/MELECON64486.2026.11418832},
	author = {Verstraete, J. and Francken, N. and Jan Sijbers and Jan De Beenhouwer}
}
@article {2432,
	title = {Investigating the Influence of Individual Physical Effects on Dimensional Measurement Deviations Using XCT Simulations},
	journal = {Measurement,},
	volume = {263},
	year = {2026},
	doi = {https://doi.org/10.1016/j.measurement.2025.120168},
	author = {Miroslav Yosifov and Thiago Linhares Fernandes and Filippo Zanini and Simone Carmignato and Jan De Beenhouwer and Jan Sijbers and Johann Kastner and Christoph Heinzl}
}
@article {2457,
	title = {Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3{\textemdash}Ex vivo imaging: Data processing, comparisons with microscopy, and tractography},
	journal = {Magnetic Resonance in Medicine},
	volume = {93},
	year = {2025},
	month = {Jan-06-2025},
	pages = {2561 - 2582},
	issn = {0740-3194},
	doi = {10.1002/mrm.v93.610.1002/mrm.30424},
	url = {https://onlinelibrary.wiley.com/toc/15222594/93/6https://onlinelibrary.wiley.com/doi/10.1002/mrm.30424https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.30424},
	author = {Schilling, Kurt G. and Howard, Amy F. D. and Grussu, Francesco and Ianus, Andrada and Hansen, Brian and Barrett, Rachel L. C. and Aggarwal, Manisha and Michielse, Stijn and Nasrallah, Fatima and Syeda, Warda and Wang, Nian and Veraart, Jelle and Roebroeck, Alard and Bagdasarian, Andrew F. and Eichner, Cornelius and Sepehrband, Farshid and Zimmermann, Jan and Soustelle, Lucas and Bowman, Christien and Tendler, Benjamin C. and Hertanu, Andreea and Ben Jeurissen and Verhoye, Marleen and Frydman, Lucio and van de Looij, Yohan and Hike, David and Dunn, Jeff F. and Miller, Karla and Landman, Bennett A. and Shemesh, Noam and Anderson, Adam and McKinnon, Emilie and Farquharson, Shawna and Dell{\textquoteright}Acqua, Flavio and Pierpaoli, Carlo and Drobnjak, Ivana and Leemans, Alexander and Harkins, Kevin D. and Descoteaux, Maxime and Xu, Duan and Huang, Hao and Santin, Mathieu D. and Grant, Samuel C. and Obenaus, Andre and Kim, Gene S. and Wu, Dan and Le Bihan, Denis and Blackband, Stephen J. and Ciobanu, Luisa and Els Fieremans and Bai, Ruiliang and Leergaard, Trygve B. and Zhang, Jiangyang and Dyrby, Tim B. and Johnson, G. Allan and Cohen-Adad, Julien and Budde, Matthew D. and Jelescu, Ileana O.}
}
@article {2456,
	title = {Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2{\textemdash}Ex vivo imaging: Added value and acquisition},
	journal = {Magnetic Resonance in Medicine},
	volume = {93},
	year = {2025},
	month = {Jan-06-2025},
	pages = {2535 - 2560},
	issn = {0740-3194},
	doi = {10.1002/mrm.v93.610.1002/mrm.30435},
	url = {https://onlinelibrary.wiley.com/toc/15222594/93/6https://onlinelibrary.wiley.com/doi/10.1002/mrm.30435https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.30435},
	author = {Schilling, Kurt G. and Grussu, Francesco and Ianus, Andrada and Hansen, Brian and Howard, Amy F. D. and Barrett, Rachel L. C. and Aggarwal, Manisha and Michielse, Stijn and Nasrallah, Fatima and Syeda, Warda and Wang, Nian and Veraart, Jelle and Roebroeck, Alard and Bagdasarian, Andrew F. and Eichner, Cornelius and Sepehrband, Farshid and Zimmermann, Jan and Soustelle, Lucas and Bowman, Christien and Tendler, Benjamin C. and Hertanu, Andreea and Ben Jeurissen and Verhoye, Marleen and Frydman, Lucio and van de Looij, Yohan and Hike, David and Dunn, Jeff F. and Miller, Karla and Landman, Bennett A. and Shemesh, Noam and Anderson, Adam and McKinnon, Emilie and Farquharson, Shawna and Dell{\textquoteright}Acqua, Flavio and Pierpaoli, Carlo and Drobnjak, Ivana and Leemans, Alexander and Harkins, Kevin D. and Descoteaux, Maxime and Xu, Duan and Huang, Hao and Santin, Mathieu D. and Grant, Samuel C. and Obenaus, Andre and Kim, Gene S. and Wu, Dan and Le Bihan, Denis and Blackband, Stephen J. and Ciobanu, Luisa and Els Fieremans and Bai, Ruiliang and Leergaard, Trygve B. and Zhang, Jiangyang and Dyrby, Tim B. and Johnson, G. Allan and Cohen-Adad, Julien and Budde, Matthew D. and Jelescu, Ileana O.}
}
@article {2455,
	title = {Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 1: In vivo small-animal imaging},
	journal = {Magnetic Resonance in Medicine},
	volume = {93},
	year = {2025},
	month = {Jan-06-2025},
	pages = {2507 - 2534},
	issn = {0740-3194},
	doi = {10.1002/mrm.v93.610.1002/mrm.30429},
	url = {https://onlinelibrary.wiley.com/toc/15222594/93/6https://onlinelibrary.wiley.com/doi/10.1002/mrm.30429https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.30429},
	author = {Jelescu, Ileana O. and Grussu, Francesco and Ianus, Andrada and Hansen, Brian and Barrett, Rachel L. C. and Aggarwal, Manisha and Michielse, Stijn and Nasrallah, Fatima and Syeda, Warda and Wang, Nian and Veraart, Jelle and Roebroeck, Alard and Bagdasarian, Andrew F. and Eichner, Cornelius and Sepehrband, Farshid and Zimmermann, Jan and Soustelle, Lucas and Bowman, Christien and Tendler, Benjamin C. and Hertanu, Andreea and Ben Jeurissen and Verhoye, Marleen and Frydman, Lucio and van de Looij, Yohan and Hike, David and Dunn, Jeff F. and Miller, Karla and Landman, Bennett A. and Shemesh, Noam and Anderson, Adam and McKinnon, Emilie and Farquharson, Shawna and Dell{\textquoteright}Acqua, Flavio and Pierpaoli, Carlo and Drobnjak, Ivana and Leemans, Alexander and Harkins, Kevin D. and Descoteaux, Maxime and Xu, Duan and Huang, Hao and Santin, Mathieu D. and Grant, Samuel C. and Obenaus, Andre and Kim, Gene S. and Wu, Dan and Le Bihan, Denis and Blackband, Stephen J. and Ciobanu, Luisa and Els Fieremans and Bai, Ruiliang and Leergaard, Trygve B. and Zhang, Jiangyang and Dyrby, Tim B. and Johnson, G. Allan and Cohen-Adad, Julien and Budde, Matthew D. and Schilling, Kurt G.}
}
@inproceedings {2401,
	title = {Correcting for focal spot drift in edge illumination X-ray phase contrast imaging},
	booktitle = {14th Conference on Industrial Computed Tomography (iCT), 4 - 7 February 2025, Antwerp, Belgium},
	year = {2025},
	doi = {doi.org/10.58286/30746},
	author = {Nicholas Francken and Jonathan Sanctorum and Ben Huyge and Jan Sijbers and Jan De Beenhouwer}
}
@article {2383,
	title = {Degradation Detection in Rice Products via Shape Variations in XCT Simulation-Empowered AI},
	journal = {Journal of Nondestructive Evaluation},
	volume = {44},
	year = {2025},
	doi = {https://doi.org/10.1007/s10921-024-01147-9},
	author = {Miroslav Yosifov and Thomas Lang and Virginia Florian and Stefan Gerth and Jan De Beenhouwer and Jan Sijbers and Johann Kastner and Christoph Heinzl}
}
@mastersthesis {2415,
	title = {Edge illumination X-ray phase contrast imaging: Advancements in simulations and inline acquisitions},
	volume = {PhD in Sciences: Physics},
	year = {2025},
	type = {PhD thesis},
	author = {Nicholas Francken}
}
@article {2417,
	title = {Edge illumination X-ray phase contrast imaging with continuous mask motion},
	journal = {Optics Express},
	volume = {33},
	year = {2025},
	pages = {41271-41286},
	doi = {https://doi.org/10.1364/OE.570476},
	author = {Ben Huyge and Nicholas Francken and Joaquim Sanctorum and Jonathan Sanctorum and Jan De Beenhouwer and Jan Sijbers}
}
@article {2385,
	title = {Efficient X-ray dark field contrast simulations using a condensed history approach},
	journal = {Optics Express},
	volume = {33},
	year = {2025},
	month = {01/2025},
	pages = {3562-3576},
	doi = {10.1364/OE.544864},
	url = {https://opg.optica.org/oe/fulltext.cfm?uri=oe-33-2-3562\&id=567367},
	author = {Nicholas Francken and Jonathan Sanctorum and Ben Huyge and Jan Sijbers and Jan De Beenhouwer}
}
@conference {2452,
	title = {Enhancing AdAPTS: Fast Field Evaporation Simulation with Parametric Local Electrodes for Atom Probe Tomography},
	year = {2025},
	abstract = {Atom probe tomography (APT) is a powerful technique for analyzing the composition of materials at the atomic level. However, no reconstruction method currently fully capitalizes on the spatial resolution potential of APT instrumentation. A model of field evaporation, efficiently and accurately describing ion trajectories, remains essential for reconstruction. To address this, we developed AdAPTS, a simulation tool that improves the efficiency of modeling individual evaporations compared to TAPSim. Both tools, however, lack a local electrode model, which influences ion trajectories. Directly incorporating a local electrode into the finite element mesh hinders simulation speed and memory efficiency. To overcome this, we introduce a local electrode feature in AdAPTS that leverages the superposition principle by projecting a solution of the field emitted by the local electrode onto a mesh of the experimental domain, resulting in constant computational overhead instead of recalculating the total electrostatic field in each iteration. The parametric definition of local electrodes allows for precise modeling of electrode geometries, providing a flexible framework for electrode design and potentially enabling more accurate 3D reconstruction. Future work will focus on integrating additional physical models in AdAPTS to expand its capabilities across diverse material systems.},
	url = {https://ge.iitm.ac.in/apt\&m-2025/schedule.html},
	author = {Julian L{\"u}ken and Claudia Fleischmann and Jan Sijbers and Jan De Beenhouwer}
}
@article {2405,
	title = {Gratings for multiresolution edge illumination X-ray phase contrast imaging: concept and simulation},
	journal = {Optics Express},
	volume = {33},
	year = {2025},
	pages = {17886-17902},
	doi = {10.1364/OE.550252},
	author = {Pieter-Jan Vanthienen and Nicholas Francken and Jonathan Sanctorum and Jan Sijbers and Jan De Beenhouwer}
}
@article {2399,
	title = {Loss of the Ubiquitin-Associated Domain of sqstm1/p62 in Zebrafish Causes a Phenotype Resembling Paget{\textquoteright}s Disease of Bone},
	journal = {Calcified Tissue International},
	volume = {116},
	year = {2025},
	pages = {1-15},
	author = {Yentl Huybrechts and Rapha{\"e}l De Ridder and Dylan Bergen and Bjorn De Samber and Eveline Boudin and Francesca Tonelli and Dries Knapen and Lucia Vergauwen and Dorien Schepers and Evelien Van Dijck and Qiao Tong and Anja Verhulst and Jan De Beenhouwer and Jan Sijbers and Chrissy Hammond and Antonella Forlino and Geert Mortier and Paul Coucke and P Eckhard Witten and Ronald Young Kwon and Andy Willaert and Gretl Hendrickx and Wim Van Hul}
}
@article {2434,
	title = {Moisture Content Estimation of Porous Building Stones using Hyperspectral Imaging},
	journal = {Scientific Data},
	volume = {13},
	year = {2025},
	month = {Dec},
	pages = {102},
	abstract = {Moisture poses a major threat to built heritage through processes such as frost damage, salt crystallization and biological growth, which accelerate stone deterioration. Stone moisture content can be determined non-destructively by spectral reflectance in the shortwave infrared (SWIR) wavelength range. To validate this, large cubic and small cylindrical samples from six stone types, Brick, Euville, Massangis, Neubrunn, Obernkirchen, and Savonni{\`e}res, with different controlled moisture levels were prepared, and a comprehensive SWIR hyperspectral image dataset was created. The acquired hyperspectral images were processed using the Normalized Relative Arc Lengths (NRAL) method to generate moisture maps that illustrate the spatial distribution of water within each sample. Because moisture distribution is influenced by pore characteristics and grain arrangement, the moisture maps were validated through petrographic examination. For quantitative validation, the mean moisture content of each sample was compared with the corresponding gravimetric moisture content. The results demonstrated strong agreement between the estimated and gravimetric moisture values, with root mean square errors ranging from 1 and 2 g/g ~{\texttimes} 100.},
	issn = {2052-4463},
	doi = {10.1038/s41597-025-06416-4},
	url = {https://doi.org/10.1038/s41597-025-06416-4},
	author = {Chaghdo, Danish Ali and Koirala, Bikram and Cristina, Laura and De Kock, Tim and Fontaine, Laurent and Hayen, Roald and Paul Scheunders}
}
@article {2425,
	title = {Superimposing Synthetic Defects into Real XCT Data and Segmentation-Based Comparison for Advanced Probability of Detection Evaluation},
	journal = { Journal of Nondestructive Evaluation },
	volume = {44},
	year = {2025},
	doi = {https://doi.org/10.1007/s10921-025-01262-1},
	author = {Miroslav Yosifov and Bernhard Fr{\"o}hler and Jan Sijbers and Jan De Beenhouwer and Johann Kastner and Christoph Heinzl}
}
@conference {2451,
	title = {AdAPTS: An Adaptive Atom Probe Tomography Simulation Library},
	year = {2024},
	abstract = {In atom probe tomography (APT), spatial reconstruction enables volumetric insight into a specimen{\textquoteright}s nanostructure. To this day, a fast reconstruction method which utilizes the true potential of APT in terms of resolution does not exist. A model of its effective inverse, the field evaporation, which provides a physically accurate description of the ion trajectories, is a crucial component in reconstruction. The simulation of each individual evaporation, such as in TAPSim, while being able to model some cases accurately, has been time inefficient. Novel methods track surface meshes, achieving better time efficiency, although at the cost of spatial accuracy.

We introduce AdAPTS, an adaptive atom probe tomography simulation library. AdAPTS is a modular volumetric finite element simulation and specimen modeling library for APT written in C++. It is capable of generating accurate detector hit maps of various specimens, efficiently representing and simulating the experimental domain from specimen to detector. Using AdAPTS, we are able to accurately simulate the field evaporation of various specimens, revealing realistic poles and zone lines.

AdAPTS utilizes a unique high quality mesh generation strategy, in which each individual atom is represented by a vertex carrying material property information (e.g. atomic mass, relative permittivity). To constitute the surrounding vacuum chamber, additional vertices are generated using efficient variable density Poisson disk sampling. The software library TetGen is used to Delaunay-tetrahedralize all generated vertices. This yields a tetrahedral mesh in which each element inherits its material properties from the material property previously assigned to each vertex. The resulting vacuum vertices constitute less than 2\% of the total vertices, effectively allowing for a fast and full-scale simulation without employing the finite element method/boundary element method (FEM/BEM) coupling scheme proposed by Fletcher et al. Simultaneously, this method provides a rigid surface notion that preserves local protrusions due to lattice nanostructure similar to TAPSim by Oberdorfer et al., which in turn preserves zone lines and poles on the hit map.

The modeling of a specimen comprises two steps. In the first step, individual crystal lattices can be defined using Bravais lattice descriptors (e.g. bcc, fcc), the material lattice constant and the Miller indices of the crystallic plane facing the detector. In the second step, the shape of the specimen and dopants contained within are modeled using implicit surfaces and binary set operators (e.g. union, intersection). However, for amorphous materials, the individual atomic positions can also be specified individually or generated by any other means. The height, tip radius and shank angle of an implicit  surface (a truncated cone with a quasi-hemispherical tip) that represents the specimen shape can be specified.

The modular finite element methods library MFEM is utilized to determine the electric field by solving Poisson{\textquoteright}s equation given an electric potential Dirichlet boundary condition at the base of the specimen. Using an Euler-forward scheme with variable time steps, the trajectory starting at each evaporation site is calculated. The trajectory integration is terminated when the trajectory intersects with the detector plane. To conclude, AdAPTS provides an efficient and accurate framework which combines specimen modeling with realistic field evaporation due to voltage pulses using state-of-the-art mesh generation and numerical simulation tools. A thorough quantitative comparison in terms of simulation time of the different simulators will be provided by the time of the conference.},
	url = {https://plan.events.mpg.de/event/261/contributions/1337/},
	author = {Julian L{\"u}ken and Claudia Fleischmann and Jan Sijbers and Jan De Beenhouwer}
}
@conference {2379,
	title = {AdAPTS: An Adaptive Atom Probe Tomography Simulation Library},
	volume = {30},
	year = {2024},
	doi = {https://doi.org/10.1093/mam/ozae044.017},
	author = {Julian L{\"u}ken and Claudia Fleischmann and Jan Sijbers and Jan De Beenhouwer}
}
@article {2323,
	title = {CAD-ASTRA: A versatile and efficient mesh projector for X-ray tomography with the ASTRA-toolbox},
	journal = {Optics Express},
	volume = {32},
	year = {2024},
	pages = {3425-3439},
	doi = {https://doi.org/10.1364/OE.498194},
	author = {Pavel Paramonov and Nicholas Francken and Jens Renders and Domenico Iuso and Tim Elberfeld and Jan De Beenhouwer and Jan Sijbers}
}
@inproceedings {2376,
	title = {Dynamic flat field correction in edge illumination imaging},
	booktitle = {SPIE Developments in X-Ray Tomography XV},
	volume = {13152},
	year = {2024},
	doi = {https://doi.org/10.1117/12.3028319},
	author = {Didem G{\"o}kbel Kekliko{\u g}lu and Nicholas Francken and Ben Huyge and Ziya Merdan and Jan De Beenhouwer and Jan Sijbers}
}
@article {2329,
	title = {Edge illumination x-ray phase contrast simulations using the CAD-ASTRA toolbox},
	journal = {Optics Express},
	volume = {32},
	year = {2024},
	pages = {10005-10021},
	doi = {10.1364/OE.516138},
	url = {https://opg.optica.org/oe/abstract.cfm?doi=10.1364/OE.516138},
	author = {Nicholas Francken and Jonathan Sanctorum and Pavel Paramonov and Jan Sijbers and Jan De Beenhouwer}
}
@inproceedings {2468,
	title = {Inline edge illumination through sample mask misalignment: a proof of concept},
	booktitle = {Proceedings of the 6th International Conference on X-ray and Neutron Phase Imaging with Gratings, Shenzhen, China},
	year = {2024},
	abstract = {Edge illumination (EI) is an X-ray phase contrast imaging setup that allows
measuring two additional complimentary contrasts. The setup consists of two absorbing
masks with slit shaped apertures. Typically, one of the masks is stepped during scans,
complicating the application of EI in inline settings. Current solutions exist, but require
either limiting the number of retrieved contrasts or fabricating specialized masks. In this
work, an EI scanning method with purposely misaligned conventional EI masks is
proposed to enable inline EI. Good agreement is found between conventional and inline EI
flatfield parameters, and first inline scan results are presented.},
	keywords = {X-ray phase contrast imaging},
	url = {https://files.sciconf.cn/upload/file/20240415/20240415160406_47435.pdf},
	author = {Nicholas Francken and Jan De Beenhouwer and Jan Sijbers}
}
@article {2348,
	title = {Inline edge illumination X-ray phase contrast imaging through mask misalignment},
	journal = {Optics Express},
	volume = {32},
	year = {2024},
	pages = {32048-32061},
	doi = {10.1364/OE.525730},
	author = {Nicholas Francken and Jonathan Sanctorum and Joaquim Sanctorum and Pieter-Jan Vanthienen and Jan Sijbers and Jan De Beenhouwer}
}
@inproceedings {2378,
	title = {Multi-resolution gratings for edge illumination x-ray phase contrast imaging: a simulation study},
	booktitle = {Developments in X-Ray Tomography XV},
	volume = {13152},
	year = {2024},
	pages = {1315208},
	publisher = {International Society for Optics and Photonics},
	organization = {International Society for Optics and Photonics},
	keywords = {cone-beam, edge illumination, grating design, magnification, mask, monte-carlo, multi-resolution, Phase contrast},
	doi = {10.1117/12.3025968},
	url = {https://doi.org/10.1117/12.3025968},
	author = {Pieter-Jan Vanthienen and Nicholas Francken and Jan Sijbers and Jan De Beenhouwer}
}
@conference {2449,
	title = {Simulating Atom Probe Tomography Using MFEM},
	year = {2024},
	abstract = {In atom probe tomography (APT), spatial reconstruction enables volumetric insight into a specimen{\textquoteright}s nanostructure. To this day, a fast reconstruction method which utilizes the true potential of APT in terms of resolution does not exist. A model of its effective inverse, the field evaporation, which provides a physically accurate description of the ion trajectories, is a crucial component in reconstruction. The simulation of each individual evaporation while has been time inefficient. We introduce AdAPTS, an adaptive atom probe tomography simulation library based on MFEM. AdAPTS is capable of generating accurate detector hit maps of various specimens, efficiently representing and simulating the experimental domain from specimen to detector. Using AdAPTS, we are able to accurately simulate the field evaporation of various specimens, revealing realistic poles and zone lines. },
	url = {https://mfem.org/workshop24/$\#$agenda},
	author = {Julian L{\"u}ken and Claudia Fleischmann and Jan Sijbers and Jan De Beenhouwer}
}
@inproceedings {2287,
	title = {A condensed history approach to x-ray dark field effects in edge illumination phase contrast simulations},
	booktitle = {45th Annual International Conference of the IEEE Engineering in Medicine and Biology Society},
	year = {2023},
	author = {Nicholas Francken and Jonathan Sanctorum and Jens Renders and Pavel Paramonov and Jan Sijbers and Jan De Beenhouwer}
}
@inproceedings {2293,
	title = {Defect detectability analysis via Probability of defect detection between traditional and deep learning methods in numerical simulations},
	booktitle = {e-Journal of Nondestructive Testing},
	volume = {28},
	year = {2023},
	issn = {1435-4934 },
	doi = {doi.org/10.58286/27716},
	author = {Miroslav Yosifov and Patrick Weinberger and Michael Reiter and Bernhard Fr{\"o}hler and Jan De Beenhouwer and Jan Sijbers and Johann Kastner and Christoph Heinzl}
}
@inproceedings {2299,
	title = {Enhancing industrial inspection with efficient edge illumination x-ray phase contrast simulations},
	booktitle = {IEEE EUROCON 2023 -20th International Conference on Smart Technologies, Torino, Italy},
	year = {2023},
	author = {Nicholas Francken and Pavel Paramonov and Jan Sijbers and Jan De Beenhouwer}
}
@article {2324,
	title = {A Multisensor Hyperspectral Benchmark Dataset For Unmixing of Intimate Mixtures},
	journal = {IEEE Sensors Journal},
	year = {2023},
	month = {2023/12/28},
	abstract = {Optical hyperspectral cameras capture the spectral reflectance of materials. Since many materials behave as heterogeneous intimate mixtures with which each photon interacts differently, the relationship between spectral reflectance and material composition is very complex. Quantitative validation of spectral unmixing algorithms requires high-quality ground truth fractional abundance data, which are very difficult to obtain. 

In this work, we generated a comprehensive laboratory ground truth dataset of intimately mixed mineral powders. For this, five clay powders (Kaolin, Roof clay, Red clay, mixed clay, and Calcium hydroxide) were mixed homogeneously to prepare 325 samples of 60 binary, 150 ternary, 100 quaternary, and 15 quinary mixtures. Thirteen different hyperspectral sensors have been used to acquire the reflectance spectra of these mixtures in the visible, near, short, mid, and long-wavelength infrared regions (350-15385) nm. Overlaps in wavelength regions due to the operational ranges of each sensor and variations in acquisition conditions resulted in a large amount of spectral variability. Ground truth composition is given by construction, but to verify that the generated samples are sufficiently homogeneous, XRD and XRF elemental analysis is performed. We believe these data will be beneficial for validating advanced methods for nonlinear unmixing and material composition estimation, including studying spectral variability and training supervised unmixing approaches. The datasets can be downloaded from the following link: https://github.com/VisionlabHyperspectral/Multisensor_datasets.},
	author = {Bikram Koirala and Behnood Rasti and Zakaria Bnoulkacem and Andr{\'e}a De Lima Ribeiro and Yuleika Madriz and Erik Herrmann and Arthur Gestels and Thomas De Kerf and Sandra Lorenz and Margret Fuchs and Koen Janssens and Gunther Steenackers and Richard Gloaguen and Paul Scheunders}
}
@article {2255,
	title = {Tabu-DART: A dynamic update strategy for efficient discrete algebraic reconstruction},
	journal = {The Visual Computer},
	volume = {39},
	year = {2023},
	pages = {4671{\textendash}4683},
	doi = {10.1007/s00371-022-02616-w},
	author = {Daniel Frenkel and Nathana{\"e}l Six and Jan De Beenhouwer and Jan Sijbers}
}
@article {2212,
	title = {A Bottom-Up Volume Reconstruction Method for Atom Probe Tomography},
	journal = {Microscopy and Microanalysis},
	volume = {28},
	year = {2022},
	pages = {1-14},
	doi = {10.1017/S1431927621012836},
	author = {Yu-Ting Ling and Siegfried Cools and Janusz Bogdanowicz and Claudia Fleischmann and Jan De Beenhouwer and Jan Sijbers and Wilfried Vandervorst}
}
@article {2276,
	title = {cuPARE: Parametric Reconstruction of Curved Fibres from Glass fibre-reinforced Composites},
	journal = {Nondestructive Testing and Evaluation},
	year = {2022},
	doi = {10.1080/10589759.2022.2155647},
	author = {Tim Elberfeld and Bernhard Fr{\"o}hler and Christoph Heinzl and Jan Sijbers and Jan De Beenhouwer}
}
@conference {2269,
	title = {Edge Illumination Phase Contrast Simulations Using the OptiX GPU Ray Tracing Engine},
	year = {2022},
	author = {Nicholas Francken and Pavel Paramonov and Jan Sijbers and Jan De Beenhouwer}
}
@article {2246,
	title = {Probability of Detection applied to X-ray inspection using numerical simulations},
	journal = {Nondestructive Testing and Evaluation},
	volume = {37},
	year = {2022},
	pages = {536-551},
	doi = {10.1080/10589759.2022.2071892},
	author = {Miroslav Yosifov and M. Reiter and S. Heupl and C. Gusenbauer and Bernhard Fr{\"o}hler and R. Fernandez- Gutierrez and Jan De Beenhouwer and Jan Sijbers and Johann Kastner and Christoph Heinzl}
}
@article {2249,
	title = {The sqstm1tmΔUBA zebrafish model, a proof-of-concept in vivo model for Paget{\textquoteright}s disease of bone?},
	journal = {Bone Reports},
	volume = {16},
	year = {2022},
	pages = {75-76},
	doi = {10.1016/j.bonr.2022.101483},
	author = {Yentl Huybrechts and Rapha{\"e}l De Ridder and Bjorn De Samber and Eveline Boudin and Francesca Tonelli and Dries Knapen and Dorien Schepers and Jan De Beenhouwer and Jan Sijbers and Antonella Forlino and Paul Coucke and P. Eckhard Witten and Ronald Kwon and Andy Willaert and Gretl Hendrickx and Wim Van Hul}
}
@conference {2170,
	title = {3D atomic resolution tomography from iDPC-STEM images using multiple atom model prior},
	year = {2021},
	author = {Shiva Hosseinnejad and E. G. T. Bosch and H. Kohr and I. Lazi{\'c} and V. Zharinov and E. Franken and Jan Sijbers and Jan De Beenhouwer}
}
@inbook {2154,
	title = {Chapter Eight - General conclusions and future perspectives},
	booktitle = {Advances in Imaging and Electron Physics},
	volume = {217},
	year = {2021},
	publisher = {Science Direct Elsevier},
	organization = {Science Direct Elsevier},
	chapter = {Chapter Eight - General conclusions and future perspectives},
	doi = {10.1016/bs.aiep.2021.01.008},
	author = {Annick De Backer and Jarmo Fatermans and Arnold Jan den Dekker and Sandra Van Aert}
}
@inbook {2152,
	title = {Chapter Five - Optimal experiment design for nanoparticle atom counting from ADF STEM images},
	booktitle = {Advances in Imaging and Electron Physics},
	volume = {217},
	year = {2021},
	publisher = {Science Direct Elsevier},
	organization = {Science Direct Elsevier},
	chapter = {Chapter Five - Optimal experiment design for nanoparticle atom counting from ADF STEM images},
	doi = {10.1016/bs.aiep.2021.01.005},
	author = {Annick De Backer and Jarmo Fatermans and Arnold Jan den Dekker and Sandra Van Aert}
}
@inbook {2150,
	title = {Chapter Four - Atom counting},
	booktitle = {Advances in Imaging and Electron Physics,},
	volume = {217},
	year = {2021},
	publisher = {Science Direct Elsevier},
	organization = {Science Direct Elsevier},
	chapter = {Chapter Four - Atom counting},
	doi = {10.1016/bs.aiep.2021.01.004},
	author = {Annick De Backer and Jarmo Fatermans and Arnold Jan den Dekker and Sandra Van Aert}
}
@inbook {2149,
	title = {Chapter One - Introduction},
	booktitle = {Advances in Imaging and Electron Physics},
	volume = {217},
	year = {2021},
	publisher = {Science Direct Elsevier},
	organization = {Science Direct Elsevier},
	chapter = {One-introduction},
	doi = {10.1016/bs.aiep.2021.01.001},
	author = {Annick De Backer and Jarmo Fatermans and Arnold Jan den Dekker and Sandra Van Aert}
}
@inbook {2153,
	title = {Chapter Seven - Image-quality evaluation and model selection with maximum a posteriori probability},
	booktitle = {Advances in Imaging and Electron Physics},
	volume = {217},
	year = {2021},
	publisher = {Science Direct Elsevier},
	organization = {Science Direct Elsevier},
	chapter = {Chapter Seven - Image-quality evaluation and model selection with maximum a posteriori probability},
	doi = {10.1016/bs.aiep.2021.01.007},
	author = {Jarmo Fatermans and Annick De Backer and Arnold Jan den Dekker and Sandra Van Aert}
}
@inbook {2156,
	title = {Chapter Six - Atom column detection},
	booktitle = {Advances in Imaging and Electron Physics},
	volume = {217},
	year = {2021},
	publisher = {Science Direct Elsevier},
	organization = {Science Direct Elsevier},
	chapter = {Chapter Six - Atom column detection},
	doi = {10.1016/bs.aiep.2021.01.006},
	author = {Jarmo Fatermans and Annick De Backer and Arnold Jan den Dekker and Sandra Van Aert}
}
@inbook {2155,
	title = {Chapter Three - Efficient fitting algorithm},
	booktitle = {Advances in Imaging and Electron Physics},
	volume = {217},
	year = {2021},
	publisher = {Science Direct Elsevier},
	organization = {Science Direct Elsevier},
	chapter = {Chapter Three - Efficient fitting algorithm},
	doi = {10.1016/bs.aiep.2021.01.003},
	author = {Annick De Backer and Jarmo Fatermans and Arnold Jan den Dekker and Sandra Van Aert}
}
@inbook {2151,
	title = {Chapter Two - Statistical parameter estimation theory: principles and simulation studies},
	booktitle = {Advances in Imaging and Electron Physics},
	volume = {217},
	year = {2021},
	publisher = {Science Direct Elsevier},
	organization = {Science Direct Elsevier},
	chapter = {Chapter Two - Statistical parameter estimation theory: principles and simulation studies},
	doi = {10.1016/bs.aiep.2021.01.002},
	author = {Annick De Backer and Jarmo Fatermans and Arnold Jan den Dekker and Sandra Van Aert}
}
@article {2049,
	title = {Diffusion Tensor Imaging of the Anterior Cruciate Ligament Following Primary Repair with Internal Bracing: a Longitudinal Study},
	journal = {Journal of Orthopaedic Research },
	volume = {39},
	year = {2021},
	pages = {1318{\textendash}1330},
	doi = {10.1002/jor.24684},
	author = {Pieter Van Dyck and Martijn Froeling and Christiaan H.W. Heusdens and Jan Sijbers and Annemie Ribbens and Thibo Billiet}
}
@article {2179,
	title = {On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: chronicles of the MEMENTO challenge},
	journal = {NeuroImage},
	volume = {240},
	year = {2021},
	doi = {https://doi.org/10.1016/j.neuroimage.2021.118367},
	author = {Alberto De Luca and Andrada Ianus and Alexander Leemans and Marco Palombo and Noam Shemesh and Hui Zhang and Daniel C Alexander and Markus Nilsson and Martijn Froeling and Geert-Jan Biessels and Mauro Zucchelli and Matteo Frigo and Enes Albay and Sara Sedlar and Abib Alimi and Samuel Deslauriers-Gauthier and Rachid Deriche and Rutger Fick and Maryam Afzali and Tomasz Pieciak and Fabian Bogusz and Santiago Aja-Fernandez and Evren Ozarslan and Derek K. Jones and Haoze Chen and Mingwu Jin and Zhijie Zhang and Fenxiang Wang and Vishwesh Nath and Prasanna Parvathaneni and Jan Morez and Jan Sijbers and Ben Jeurissen and Shreyas and Fadnavis and Stefan Endres and Ariel Rokem and Eleftherios Garyfallidis and Irina Sanchez and Vesna Prchkovska and Paulo Rodrigues and Bennet A. Landman and Kurt G Schilling}
}
@inproceedings {2157,
	title = {Tabu-DART: a dynamic update strategy for the Discrete Algebraic Reconstruction Technique based on Tabu-search},
	booktitle = { International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine},
	year = {2021},
	author = {Daniel Frenkel and Jan De Beenhouwer and Jan Sijbers}
}
@conference {2081,
	title = {3D Atomic Scale Quantification of Nanostructures and their Dynamics Using Model-based STEM},
	year = {2020},
	author = {Sandra Van Aert and Annick De Backer and De wael, A and Jarmo Fatermans and Friedrich, T and Ivan Lobato and O{\textquoteright}Leary, C M. and Varambhia, A and Thomas Altantzis and Jones, L and Arnold Jan den Dekker and Peter D Nellist and Sara Bals}
}
@inproceedings {1979,
	title = {An adaptive probability map for the Discrete Algebraic Reconstruction Technique},
	booktitle = {10th Conference on Industrial Computed Tomography (ICT 2020)},
	year = {2020},
	pages = {1-6},
	author = {Daniel Frenkel and Jan De Beenhouwer and Jan Sijbers}
}
@article {2057,
	title = {Analysis and Comparison of Algorithms for the Tomographic Reconstruction of Curved Fibres},
	journal = {Nondestructive Testing and Evaluation},
	volume = {35},
	year = {2020},
	pages = {328-341},
	doi = {https://doi.org/10.1080/10589759.2020.1774583},
	author = {Bernhard Fr{\"o}hler and Tim Elberfeld and Torsten M{\"o}ller and Hans-Christian Hege and Jan De Beenhouwer and Jan Sijbers and Johann Kastner and Christoph Heinzl}
}
@inproceedings {2084,
	title = {Aperture size selection for improved brain tumor detection and quantification in multi-pinhole 123I-CLINDE SPECT imaging},
	booktitle = {IEEE Nuclear Science Symposium and Medical Imaging Conference, Boston, USA (2020)},
	year = {2020},
	author = {Benjamin Auer and Kesava Kalluri and Aly H. Abayazeed and Jan De Beenhouwer and Navid Zeraatkar and Clifford Lindsay and Neil Momsen and R. Garrett Richards and Micaehla May and Matthew A. Kupinski and Philip H. Kuo and Lars R. Furenlid and Michael A. King}
}
@article {2063,
	title = {Atom column detection from simultaneously acquired ABF and ADF STEM images},
	journal = {Ultramicroscopy},
	volume = {219},
	year = {2020},
	pages = {113046},
	doi = {https://doi.org/10.1016/j.ultramic.2020.113046},
	author = {Fatermans, J. and Arnold Jan den Dekker and M{\"u}ller-Caspary, K. and N Gauquelin and Jo Verbeeck and Sandra Van Aert}
}
@conference {2091,
	title = {Bayesian model selection for atom column detection from ABF-ADF STEM images},
	year = {2020},
	author = {Fatermans, J. and Arnold Jan den Dekker and N Gauquelin and Jo Verbeeck and Sandra Van Aert}
}
@article {2032,
	title = {Co valence transformation in isopolar LaCoO3/LaTiO3 perovskite heterostructures via interfacial engineering},
	journal = {Phys. Rev. Materials},
	volume = {4},
	year = {2020},
	chapter = {026001},
	doi = {https://doi.org/10.1103/PhysRevMaterials.4.026001},
	author = {G Araizi-Kanoutas and J Geessinck and N Gauquelin and S Smit and X H Verbeeck and S K Mishra and P Bencok and C Schlueter and T-L Lee and D Krishnan and J Fatermans and Jo Verbeeck and G Rijnders and G Koster and M S Golden}
}
@article {2064,
	title = {Diffusion tensor imaging of the anterior cruciate ligament graft following reconstruction: a longitudinal study},
	journal = {European Radiology},
	volume = {34},
	year = {2020},
	pages = {6673{\textendash}6684},
	doi = {10.1007/s00330-020-07051-w},
	author = {Pieter Van Dyck and Thibo Billiet and Damien Desbuquoit and Peter Verdonk and Christiaan H. Heusdens and Ella Roelant and Jan Sijbers and Martijn Froeling}
}
@article {2083,
	title = {Keel-Edge Height Selection for Improved Multi-Pinhole 123I Brain SPECT Imaging},
	journal = {Journal of Nuclear Medicine},
	volume = {61},
	year = {2020},
	pages = {573},
	abstract = {573Objectives: Given its excellent resolution versus sensitivity trade-off, multi-pinhole SPECT has become a powerful tool for clinical imaging of small human structures such as the brain [1]. Our research team is designing and constructing a next-generation multi-pinhole system, AdaptiSPECT-C, for quantitative brain imaging. In this context, keel-edge pinhole has proven to increase significantly attenuation of gamma rays through the edges of the pinhole aperture compared to the most commonly clinically used knife-edge profile [2-4]. In this work, we investigate the potential improvement in imaging performance of multiple keel-edge pinhole profiles as a function of keel height for AdaptiSPECT-C compared to a knife-edge collimation for 123I-IMP brain perfusion. Methods: The prototype AdaptiSPECT-C system used herein is composed of 23 hexagonal detector modules hemi-spherically arranged along 3 rings. For modeling in GATE simulation (GS) [5], each of these modules is composed of 1.5 mm radius pinhole and a 1 cm thick NaI(Tl) crystal with a 5 cm thick back-scattering compartment, which was considered to simulate 123I down-scatter interactions. Multiple keel-edge heights, corresponding to 0.0 (knife edge), 0.375, 0.75, 1.0, 1.125, 1.5, 1.875, and 2.25 mm were studied. We evaluated the volumetric sensitivity and relative amount of collimator penetration for a 15\% energy window centered at 159 keV in simulated projections of a 21 cm diameter spherical source (e.g. corresponding to the system{\textquoteright}s volume of interest) centered at the focal point of the pinholes. For reconstruction, an approach developed in our group was employed for modeling using GS the system response and especially collimator penetration into the system matrix [6,7] for the knife and the keel-edge designs. An XCAT [8] brain phantom with source distribution for the perfusion imaging agent 123I-IMP was simulated using the pinhole designs. Projection were acquired considering two scenarios: noise free (S1), and equal imaging time comparison for a realistic clinical scan time (e.g. 30 min [9,10]) (S2). Reconstructions were performed with a customized 3D-MLEM software into images of 1203 voxels of (2 mm)3. The reconstructed images were then compared to the ground truth image in terms of the normalized root mean squared error (NRMSE) and activity recovery (\%AR) for selected three-dimensional brain regions. Results: A keel-edge height of 0.375-0.75 mm represents the best choice leading to a significant reduction of the amount of penetration (up to  50\%) at the expense of sensitivity (-20\%) compared to a knife-edge profile. Visually, for all scenarios, the use of such a keel-edge profile leads to better separation of the brain structures, especially the caudate and the putamen. When sensitivity is not taken into account (e.g. noise free scenario), increasing the keel height improves NRMSE results. For an equal imaging time comparison, lowest NRMSE values are achieved for a 0.375-0.75 mm keel-height. A further keel-height increase degrades the NRMSE results due to significant loss of counts compared to knife-edge design. A 0.75 mm keel height leads on average to the best \%ARs (e.g. closest value to 100\%), especially for the striatum and putamen. For cortex and cerebellum regions, \%ARs are comparable with those obtained for a knife-edge design. Conclusion: In this work, we demonstrated that the use of a  0.75 mm height keel-edge profile for AdaptiSPECT-C incorporating 1.5 mm radius pinholes leads to superior imaging performance compared to knife-edge collimation for clinical 123I brain perfusion imaging. A range of aperture radii from 0.5 to 3.5 mm for each design have been investigated and will be shown at the time of the conference. We are currently working on performing a numerical-observer task-performance study of defect-detection in perfusion. Research Support: National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Grant No R01 EB022521. Volumetric Sensitivities, Amount of Penetration, and Lowest NRMSE for the designs investigated},
	url = {http://jnm.snmjournals.org/content/61/supplement_1/573.abstract},
	author = {Benjamin Auer and Kesava Kalluri and Jan De Beenhouwer and Navid Zeraatkar and Neil Momsen and Philip H. Kuo and Lars R. Furenlid and Michael A. King}
}
@article {2134,
	title = {Proposing a gamma radiation based intelligent system for simultaneous analyzing and detecting type and amount of petroleum by-products},
	journal = {Nuclear Engineering and Technology},
	year = {2020},
	type = {Research regular paper},
	abstract = {It is important for operators of poly-pipelines in petroleum industry to continuously monitor characteristics of transferred fluid such as its type and amount. To achieve this aim, in this study a dual energy gamma attenuation technique in combination with artificial neural network (ANN) is proposed to simultaneously determine type and amount of four different petroleum by-products. The detection system is composed of a dual energy gamma source, including americium-241 and barium-133 radioisotopes, and one 2.54 cm {\texttimes} 2.54 cm sodium iodide detector for recording the transmitted photons. Two signals recorded in transmission detector, namely the counts under photo peak of Americium-241 with energy of 59.5 keV and the counts under photo peak of Barium-133 with energy of 356 keV, were applied to the ANN as the two inputs and volume percentages of petroleum by-products were assigned as the outputs.},
	author = {Mohammadmehdi Roshani and Giang Phan and Rezhna Hassan Faraj and Nhut-Huan Phan and Gholam Hossein Roshani and Enrico Corniani and Ehsan Nazemi}
}
@article {2082,
	title = {Reconstruction using Depth of Interaction Information of Curved and Flat Detector Designs for Quantitative Multi-Pinhole Brain SPECT},
	journal = {Journal of Nuclear Medicine},
	volume = {61},
	year = {2020},
	pages = {103},
	abstract = {103Objectives: Brain SPECT has many clinical applications, especially for cerebral blood flow and dopamine transporter imaging [1,2]. In this context, a dedicated brain imaging, multi-pinhole system, AdaptiSPECT-C, is being developed by our group. Recent studies in cardiac and small animal imaging have demonstrated that the use of curved detector could improve image quality, by reducing parallax errors due to the depth of interaction (DOI) effect [3,4]. In this simulation study, we proposed to investigate using reconstruction with DOI modeling the potential advantage in imaging performance of curved over flat detectors for 123I-IMP perfusion imaging using the AdaptiSPECT-C system. Methods: The AdaptiSPECT-C design used in this work consists of 26 detector modules, 158 by 158 mm2 in size, arranged around the patient{\textquoteright}s head in three rings. The simulated detector modules were composed of a 8 mm thick NaI(Tl) crystal coupled to a 5 cm thick back-scattering compartment, representing components behind the crystal, to model 123I down-scatter interactions. Each detector module is associated with a 1.36 mm radius direct knife-edge pinhole aperture collimator. Two different system designs were considered, one based on curved detectors, and the other on flat detectors. The curved detectors were designed so that the radius of curvature corresponds to the detector to system center distance (e.g. 30.5 cm). This distance was the same for the flat detectors. GATE simulation [5] was employed to compute the system matrix [6,7] for both detector designs by forming the system response for the activity within each three-dimensional image-voxel of a 24 cm diameter sphere, thus including DOI variations and corrections in reconstruction [6,7]. An XCAT brain phantom [8] emulating 123I-IMP perfusion source distribution was simulated using the two designs. Data were acquired following three scenarios: noise free case (S1), equal number of counts comparison (S2) (e.g. 5.5M detected counts [9]), and equal imaging time comparison for the typical scan time (e.g. 30 min [10]) (S3). For S3, the total number of counts for the curved and flat detector designs, were respectively 9.24M and 9.17M. Projections were reconstructed with 3D-MLEM into images of 1203 voxels of (2 mm)3 and reconstruction compared to the ground truth image. The normalized root mean squared error (NRMSE) as well as percentage of activity recovery (\%AR) for several brain regions were used to evaluate the image quality. Results: Only a small gain in volumetric sensitivity ( 0.8\%) was obtained with the curved detector design. Qualitatively, the reconstructions for the curved and flat detector designs appear similar for all the 3 noise scenarios. Differences are mostly for the peripheral regions of the head where the differences in the obliquity of the gamma-rays passing through the apertures would be the greatest. Due to lower activity, those regions are also more impacted by noise. Quantitatively, a slight NRMSE improvement using curved detectors was seen. The curved detector design leads on average to the best ARs, especially for the striatum and putamen. Regions at the edges of the brain (e.g. cortex and cerebellum), more impacted by DOI effect, are similarly recovered by the two designs. Conclusion: We demonstrated that using curved instead of flat detector for AdaptiSPECT-C with solely centered pinholes leads to small improvement in sensitivity and image quality based on visual inspection, NRMSE, and activity recovery analysis. Flat detector associated with a sophisticated DOI correction was found to lead to similar results than those obtained with the curved detector. Further investigation will be performed using additional pinholes irradiating the 4 quadrants of the detectors which will increase the obliquity of the rays striking the detectors and may thus result in larger difference. Research Support: Grant No R01 EB022521 (NIBIB).},
	url = {http://jnm.snmjournals.org/content/61/supplement_1/103.abstract},
	author = {Benjamin Auer and Kesava Kalluri and Jan De Beenhouwer and Kimberly Doty and Navid Zeraatkar and Philip H. Kuo and Lars R. Furenlid and Michael A. King}
}
@conference {2094,
	title = {Strategies for quantifying the 3D atomic structure and the dynamics of nanomaterials using model-based STEM},
	year = {2020},
	author = {Sandra Van Aert and Annick De Backer and De wael, A and Jarmo Fatermans and Arslan Irmak, E and Friedrich, T and Ivan Lobato and Jones, L and Arnold Jan den Dekker and Peter D Nellist and Sara Bals}
}
@conference {1974,
	title = {Atom column detection from STEM images using the maximum a posteriori probability rule},
	year = {2019},
	author = {J Fatermans and Arnold Jan den Dekker and O{\textquoteright}Leary, C M. and Peter D Nellist and Sandra Van Aert}
}
@conference {1975,
	title = {Atom detection from electron microscopy images},
	year = {2019},
	pages = {15},
	author = {J Fatermans and Arnold Jan den Dekker and Sandra Van Aert}
}
@inproceedings {1918,
	title = {An Interactive Visual Comparison Tool for 3D Volume Datasets represented by Nonlinearly Scaled 1D Line Plots through Space-filling Curves},
	booktitle = {9th Conference on Industrial Computed Tomography},
	year = {2019},
	address = {Padova, Italy},
	author = {Johannes Weissenb{\"o}ck and Bernhard Fr{\"o}hler and Eduard Gr{\"o}ller and Jonathan Sanctorum and Jan De Beenhouwer and Jan Sijbers and Santhosh Ayalur Karunakaran and Helmuth Hoeller and Johann Kastner and Christoph Heinzl}
}
@inproceedings {1989,
	title = {Investigation of a Monte Carlo simulation and an analytic-based approach for modeling the system response for clinical I-123 brain SPECT imaging},
	booktitle = {15th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine},
	volume = {11072},
	year = {2019},
	pages = {187 {\textendash} 190},
	publisher = {International Society for Optics and Photonics},
	organization = {International Society for Optics and Photonics},
	keywords = {image reconstruction, Monte-Carlo simulation, SPECT I-123 brain imaging, System response modeling, Variance reduction technique (forced detection)},
	doi = {10.1117/12.2534881},
	url = {https://doi.org/10.1117/12.2534881},
	author = {Benjamin Auer and Navid Zeraatkar and Jan De Beenhouwer and Kesava Kalluri and Philip H. Kuo and Lars R. Furenlid and Michael A. King}
}
@conference {1990,
	title = {Investigation of keel versus knife edge pinhole profiles for a next-generation SPECT system dedicated to clinical brain imaging},
	year = {2019},
	month = {2019},
	author = {Benjamin Auer and Kesava Kalluri and Jan De Beenhouwer and Navid Zeraatkar and Arda K{\"o}nik and Philip H. Kuo and Lars R. Furenlid and Michael A. King}
}
@article {1925,
	title = {The maximum a posteriori probability rule for atom column detection from HAADF STEM images},
	journal = {Ultramicroscopy},
	volume = {201},
	year = {2019},
	pages = {81-91},
	abstract = {Recently, the maximum a posteriori (MAP) probability rule has been proposed as an objective and quantitative method to detect atom columns and even single atoms from high-resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images. The method combines statistical parameter estimation and model-order selection using a Bayesian framework and has been shown to be especially useful for the analysis of the structure of beam-sensitive nanomaterials. In order to avoid beam damage, images of such materials are usually acquired using a limited incoming electron dose resulting in a low contrast-to-noise ratio (CNR) which makes visual inspection unreliable. This creates a need for an objective and quantitative approach. The present paper describes the methodology of the MAP probability rule, gives its step-by-step derivation and discusses its algorithmic implementation for atom column detection. In addition, simulation results are presented showing that the performance of the MAP probability rule to detect the correct number of atomic columns from HAADF STEM images is superior to that of other model-order selection criteria, including the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC). Moreover, the MAP probability rule is used as a tool to evaluate the relation between STEM image quality measures and atom detectability resulting in the introduction of the so-called integrated CNR (ICNR) as a new image quality measure that better correlates with atom detectability than conventional measures such as signal-to-noise ratio (SNR) and CNR.},
	keywords = {Atom detectability, Atom detection, Model selection, Scanning transmission electron microscopy (STEM)},
	issn = {0304-3991},
	doi = {https://doi.org/10.1016/j.ultramic.2019.02.003},
	url = {http://www.sciencedirect.com/science/article/pii/S0304399118304236},
	author = {J Fatermans and Sandra Van Aert and Arnold Jan den Dekker}
}
@inproceedings {1873,
	title = {Moving Statistical Body Shape Models Using Blender},
	booktitle = {Proceedings of the 20th Congress of the International Ergonomics Association (IEA 2018)},
	year = {2019},
	pages = {28{\textendash}38},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	address = {Cham},
	abstract = {In this paper, we present a new framework to integrate movement acquired by a motion capture system to a statistical body shape model using Blender. This provides a visualization of a digital human model based upon anthropometry and biomechanics of the subject. A moving statistical body shape model helps to visualize physical tasks with inter-individual variability in body shapes as well as anthropometric dimensions. This parametric modeling approach is useful for reliable prediction and simulation of the body shape movement of a specific population with a few given predictors such as stature, body mass index and age.},
	isbn = {978-3-319-96077-7},
	doi = {10.1007/978-3-319-96077-7_4},
	author = {Scataglini, Sofia and Femke Danckaers and Haelterman, Robby and Toon Huysmans and Jan Sijbers},
	editor = {Bagnara, Sebastiano and Tartaglia, Riccardo and Albolino, Sara and Alexander, Thomas and Fujita, Yushi}
}
@inproceedings {1988,
	title = {Preliminary investigation of attenuation and scatter correction strategies for a next-generation SPECT system dedicated to quantitative clinical brain imaging},
	booktitle = {IEEE Nuclear Science Symposium and Medical Imaging Conference},
	year = {2019},
	month = {11/2019},
	address = {Manchester, UK},
	author = {Benjamin Auer and Jan De Beenhouwer and Navid Zeraatkar and Philip H. Kuo and Lars R. Furenlid and Michael A. King}
}
@article {2085,
	title = {Primary, scatter, and penetration characterizations of parallel-hole and pinhole collimators for I-123 SPECT},
	journal = {Physics in Medicine \& Biology},
	volume = {64},
	year = {2019},
	pages = {245001},
	abstract = {Multi-pinhole (MPH) collimators are known to provide better trade-off between sensitivity and resolution for preclinical, as well as for smaller regions in clinical SPECT imaging compared to conventional collimators. In addition to this geometric advantage, MPH plates typically offer better stopping power for penetration than the conventional collimators, which is especially relevant for I-123 imaging. The I-123 emits a series of high-energy (>300 keV,  2.5\% abundance) gamma photons in addition to the primary emission (159 keV, 83\% abundance). Despite their low abundance, high-energy photons penetrate through a low-energy parallel-hole (LEHR) collimator much more readily than the 159 keV photons, resulting in large downscatter in the photopeak window. In this work, we investigate the primary, scatter, and penetration characteristics of a single pinhole collimator that is commonly used for I-123 thyroid imaging and our two MPH collimators designed for I-123 DaTscan imaging for Parkinson{\textquoteright}s Disease, in comparison to three different parallel-hole collimators through a series of experiments and Monte Carlo simulations. The simulations of a point source and a digital human phantom with DaTscan activity distribution showed that our MPH collimators provide superior count performance in terms of high primary counts, low penetration, and low scatter counts compared to the parallel-hole and single pinhole collimators. For example, total scatter, multiple scatter, and collimator penetration events for the LEHR were 2.5, 7.6 and 14 times more than that of MPH within the 15\% photopeak window. The total scatter fraction for LEHR was 56\% where the largest contribution came from the high-energy scatter from the back compartments (31\%). For the same energy window, the total scatter for MPH was 21\% with only 1\% scatter from the back compartments. We therefore anticipate that using MPH collimators, higher quality reconstructions can be obtained in a substantially shorter acquisition time for I-123 DaTscan and thyroid imaging.},
	doi = {10.1088/1361-6560/ab58fe},
	url = {https://doi.org/10.1088\%2F1361-6560\%2Fab58fe},
	author = {Arda K{\"o}nik and Benjamin Auer and Jan De Beenhouwer and Kesava Kalluri and Navid Zeraatkar and Lars R. Furenlid and Michael A. King}
}
@conference {1959,
	title = {Quantifying 3D atomic structures of nanomaterials and their dynamics using model-based scanning transmission electron microscopy},
	year = {2019},
	author = {Sandra Van Aert and De wael, A and J Fatermans and Ivan Lobato and Annick De Backer and Jones, L and Arnold Jan den Dekker and Peter D Nellist}
}
@mastersthesis {1976,
	title = {Quantitative atom detection from atomic-resolution transmission electron microscopy images},
	volume = {Doctor of Science/Physics},
	year = {2019},
	type = {PhD thesis},
	author = {J Fatermans}
}
@conference {1958,
	title = {Strategies for quantifying 3D atomic structures of nanomaterials and their dynamics using dose-efficient ADF STEM},
	year = {2019},
	author = {Sandra Van Aert and De wael, A and J Fatermans and Ivan Lobato and Annick De Backer and Jones, L and Arnold Jan den Dekker and Peter D Nellist}
}
@inproceedings {1917,
	title = {Tools for the Analysis of Datasets from X-Ray Computed Tomography based on Talbot-Lau Grating Interferometry},
	booktitle = {9th Conference on Industrial Computed Tomography},
	year = {2019},
	address = {Padova, Italy},
	url = {https://www.ndt.net/article/ctc2019/papers/iCT2019_Full_paper_52.pdf},
	author = {Bernhard Fr{\"o}hler and Lucas da Cunha Melo and Johannes Weissenb{\"o}ck and Johann Kastner and Torsten M{\"o}ller and Hans-Christian Hege and Eduard Gr{\"o}ller and Jonathan Sanctorum and Jan De Beenhouwer and Jan Sijbers and Christoph Heinzl}
}
@inproceedings {1874,
	title = {Using 3D Statistical Shape Models for Designing Smart Clothing},
	booktitle = {Proceedings of the 20th Congress of the International Ergonomics Association (IEA 2018)},
	year = {2019},
	pages = {18{\textendash}27},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	address = {Cham},
	abstract = {In this paper we present an innovative approach to design smart clothing using statistical body shape modeling (SBSM) from the CAESAR{\texttrademark} dataset. A combination of different digital technologies and applications are used to create a common co-design workflow for garment design. User and apparel product design and developers can get personalized prediction of cloth sizing, fitting and aesthetics.},
	isbn = {978-3-319-96077-7},
	doi = {10.1007/978-3-319-96077-7_3},
	author = {Scataglini, Sofia and Femke Danckaers and Haelterman, Robby and Toon Huysmans and Jan Sijbers and Andreoni, Giuseppe},
	editor = {Bagnara, Sebastiano and Tartaglia, Riccardo and Albolino, Sara and Alexander, Thomas and Fujita, Yushi}
}
@article {1923,
	title = {A Visual Tool for the Analysis of Algorithms for Tomographic Fiber Reconstruction in Materials Science},
	journal = {Computer Graphics Forum},
	volume = {38},
	year = {2019},
	pages = {273-283},
	doi = {10.1111/cgf.13688},
	author = {Bernhard Fr{\"o}hler and Tim Elberfeld and Torsten M{\"o}ller and Johannes Weissenb{\"o}ck and Jan De Beenhouwer and Jan Sijbers and Hans-Christian Hege and Johann Kastner and Christoph Heinzl}
}
@conference {1890,
	title = {Bayesian analysis of noisy scanning transmission electron microscopy images for single atom detection},
	year = {2018},
	pages = {95},
	author = {J Fatermans and Arnold Jan den Dekker and M{\"u}ller-Caspary, K and Ivan Lobato and Sandra Van Aert}
}
@conference {1957,
	title = {Maximising dose efficiency in quantitative STEM to reveal the 3D atomic structure of nanomaterials},
	year = {2018},
	author = {Sandra Van Aert and J Fatermans and Annick De Backer and van den Bos, K. H. W. and O{\textquoteright}Leary, C M. and M{\"u}ller-Caspary, K and Jones, L and Ivan Lobato and B{\'e}ch{\'e}, A and Arnold Jan den Dekker and Sara Bals and Peter D Nellist}
}
@conference {1891,
	title = {The maximum a posteriori probability rule to detect single atoms from low signal-to-noise ratio scanning transmission electron microscopy images},
	year = {2018},
	author = {J Fatermans and Arnold Jan den Dekker and M{\"u}ller-Caspary, K and Ivan Lobato and Sandra Van Aert}
}
@inproceedings {1880,
	title = {Preliminary evaluation of surface mesh modeling of system geometry, anatomy phantom, and source activity for GATE simulations},
	booktitle = {IEEE Nuclear Science Symposium and Medical Imaging Conference},
	year = {2018},
	month = {11/2018},
	address = {Sydney, Australia},
	author = {Benjamin Auer and Arda K{\"o}nik and Timothy J. Fromme and Kesava Kalluri and Jan De Beenhouwer and George I. Zubal and Lars R. Furenlid and Michael A. King}
}
@inproceedings {1879,
	title = {Preliminary investigation of design parameters of an innovative multi- pinhole system dedicated to brain SPECT imaging},
	booktitle = {IEEE Nuclear Science Symposium and Medical Imaging Conference},
	year = {2018},
	month = {11/2018},
	address = {Sydney, Australia},
	author = {Benjamin Auer and Jan De Beenhouwer and Timothy J. Fromme and Kesava Kalluri and Justin C. Goding and George I. Zubal and Lars R. Furenlid and Michael A. King}
}
@article {1877,
	title = {Simulations of a Multipinhole SPECT Collimator for Clinical Dopamine Transporter (DAT) Imaging},
	journal = {IEEE Transactions on Radiation and Plasma Medical Sciences},
	volume = {2},
	year = {2018},
	month = {Sept},
	pages = {444-451},
	keywords = {Analytical models, Apertures, Brain, Collimators, Logic gates, multipinhole (MPH), Sensitivity, simulation, Single photon emission computed tomography, SPECT},
	issn = {2469-7311},
	doi = {10.1109/TRPMS.2018.2831208},
	author = {Arda K{\"o}nik and Jan De Beenhouwer and J. M. Mukherjee and Kesava Kalluri and S Banerjee and N Zeraatkar and Timothy J. Fromme and Michael A. King}
}
@article {1878,
	title = {Single Atom Detection from Low Contrast-to-Noise Ratio Electron Microscopy Images},
	journal = {Phys. Rev. Lett.},
	volume = {121},
	year = {2018},
	month = {Jul},
	pages = {056101},
	abstract = {Single atom detection is of key importance to solving a wide range of scientific and technological problems. The strong interaction of electrons with matter makes transmission electron microscopy one of the most promising techniques. In particular, aberration correction using scanning transmission electron microscopy has made a significant step forward toward detecting single atoms. However, to overcome radiation damage, related to the use of high-energy electrons, the incoming electron dose should be kept low enough. This results in images exhibiting a low signal-to-noise ratio and extremely weak contrast, especially for light-element nanomaterials. To overcome this problem, a combination of physics-based model fitting and the use of a model-order selection method is proposed, enabling one to detect single atoms with high reliability.},
	doi = {10.1103/PhysRevLett.121.056101},
	url = {https://link.aps.org/doi/10.1103/PhysRevLett.121.056101},
	author = {J Fatermans and Arnold Jan den Dekker and M{\"u}ller-Caspary, K. and Ivan Lobato and O{\textquoteright}Leary, C. M. and Peter D Nellist and Sandra Van Aert}
}
@conference {1889,
	title = {Detection of atomic columns from noisy STEM images},
	year = {2017},
	pages = {445-446},
	author = {J Fatermans and M{\"u}ller-Caspary, K and Arnold Jan den Dekker and Sandra Van Aert}
}
@article {1744,
	title = {Diffusion Tensor Imaging of the Anterior Cruciate Ligament Graft},
	journal = {Journal of Magnetic Resonance Imaging},
	volume = {46},
	year = {2017},
	pages = {1423{\textendash}1432},
	doi = {10.1002/jmri.25666},
	author = {Pieter Van Dyck and Martijn Froeling and Eline De Smet and Pim Pullens and Micha{\"e}l Torfs and Peter Verdonk and Jan Sijbers and Paul M Parizel and Ben Jeurissen}
}
@conference {Van_Dyck2017-jo,
	title = {Diffusion Tensor Imaging of the Anterior Cruciate Ligament Graft},
	year = {2017},
	pages = {377},
	author = {Pieter Van Dyck and De Smet, Eline and Froeling, Martijn and Peter Verdonk and Torfs, Micha{\"e}l and Pim Pullens and Jan Sijbers and Paul M Parizel and Ben Jeurissen}
}
@article {1676,
	title = {Ergonomic design of an EEG headset using 3D anthropometry},
	journal = {Applied Ergonomics},
	volume = {58},
	year = {2017},
	month = {2017},
	pages = {128{\textendash}136},
	doi = {doi:10.1016/j.apergo.2016.06.002},
	author = {Daniel Lacko and Jochen Vleugels and Erik Fransen and Toon Huysmans and Guido De Bruyne and Marc M. Van Hulle and Jan Sijbers and Stijn Verwulgen}
}
@article {1718,
	title = {High angular resolution diffusion-weighted imaging in mild traumatic brain injury},
	journal = {NeuroImage: Clinical},
	volume = {13},
	year = {2017},
	month = {11/2016},
	pages = {174 - 180},
	abstract = {We sought to investigate white matter abnormalities in mild traumatic brain injury (mTBI) using diffusion-weighted magnetic resonance imaging (DW-MRI). We applied a global approach based on tract-based spatial statistics skeleton as well as constrained spherical deconvolution tractography. DW-MRI was performed on 102 patients with mTBI within two months post-injury and 30 control subjects. A robust global approach considering only the voxels with a single-fiber configuration was used in addition to global analysis of the tract skeleton and probabilistic whole-brain tractography. In addition, we assessed whether the microstructural parameters correlated with age, time from injury, patient{\textquoteright}s outcome and white matter \{MRI\} hyperintensities. We found that whole-brain global approach restricted to single-fiber voxels showed significantly decreased fractional anisotropy (FA) (p = 0.002) and increased radial diffusivity (p = 0.011) in patients with mTBI compared with controls. The results restricted to single-fiber voxels were more significant and reproducible than those with the complete tract skeleton or the whole-brain tractography. \{FA\} correlated with patient outcomes, white matter hyperintensities and age. No correlation was observed between \{FA\} and time of scan post-injury. In conclusion, the global approach could be a promising imaging biomarker to detect white matter abnormalities following traumatic brain injury.},
	keywords = {Diffusion-weighted magnetic resonance imaging, Global approach, Magnetic Resonance Imaging, probabilistic tractography, Traumatic brain injury},
	issn = {2213-1582},
	doi = {http://dx.doi.org/10.1016/j.nicl.2016.11.016},
	url = {http://www.sciencedirect.com/science/article/pii/S2213158216302248},
	author = {Mohammadian, Mehrbod and Timo Roine and Jussi Hirvonen and Timo Kurki and Henna Ala-Sepp{\"a}l{\"a} and Janek Frantz{\'e}n and Ari Katila and Anna Kyll{\"o}nen and Henna-Riikka Maanp{\"a}{\"a} and Jussi Posti and Riikka Takala and Jussi Tallus and Olli Tenovuo}
}
@article {1793,
	title = {An alternative approach for ζ-factor measurement using pure element nanoparticles},
	journal = {Ultramicroscopy},
	volume = {164},
	year = {2016},
	pages = {11{\textendash}16},
	abstract = {It is very challenging to measure the chemical composition of hetero nanostructures in a reliable and quantitative manner. Here, we propose a novel and straightforward approach that can be used to quantify energy dispersive X-ray spectra acquired in a transmission electron microscope. Our method is based on a combination of electron tomography and the so-called ζ-factor technique. We will demonstrate the reliability of our approach as well as its applicability by investigating Au-Ag and Au-Pt hetero nanostructures. Given its simplicity, we expect that the method could become a new standard in the field of chemical characterization using electron microscopy.},
	keywords = {Bimetallic nanoparticles, EDXS quantification, Electron tomography},
	issn = {03043991},
	doi = {10.1016/j.ultramic.2016.03.002},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0304399116300134},
	author = {Daniele Zanaga and Thomas Altantzis and Jonathan Sanctorum and Bert Freitag and Sara Bals}
}
@conference {1888,
	title = {Bayesian model-order selection in electron microscopy to detect atomic columns in noisy images},
	year = {2016},
	pages = {53},
	author = {J Fatermans and Sandra Van Aert and Arnold Jan den Dekker}
}
@article {1763,
	title = {Denoising of diffusion MRI using random matrix theory},
	journal = {NeuroImage},
	volume = {142},
	year = {2016},
	pages = {384-396},
	doi = {10.1016/j.neuroimage.2016.08.016},
	author = {Jelle Veraart and Dmitry S. Novikov and Christiaens Daan and Ades-Aron, Benjamin and Jan Sijbers and Els Fieremans}
}
@article {1620,
	title = {Diffusion kurtosis imaging probes cortical alterations and white matter pathology following cuprizone-induced demyelination and spontaneous remyelination},
	journal = {NeuroImage},
	volume = {125},
	year = {2016},
	pages = {363{\textendash}377},
	doi = {10.1016/j.neuroimage.2015.10.052},
	author = {Caroline Guglielmetti and Jelle Veraart and Ella Roelant and Zhenhua Mai and Jasmijn Daans and Johan Van Audekerke and Maarten Naeyaert and Greetje Vanhoutte and Rafael  Delgado Y Palacios and Jelle Praet and Els Fieremans and Peter Ponsaerts and Jan Sijbers and Annemie Van Der Linden and Marleen Verhoye}
}
@conference {1597,
	title = {Gibbs ringing removal in diffusion MRI using second order total variation minimization},
	volume = {23},
	year = {2015},
	pages = {2809},
	author = {Jelle Veraart and Florian Knoll and Jan Sijbers and Els Fieremans and Dmitry S. Novikov}
}
@inproceedings {2043,
	title = {SPIE ProceedingsEnergy calibration of photon counting detectors using x-ray tube potential as a reference for material decomposition applications},
	booktitle = {SPIE Medical ImagingMedical Imaging 2015: Physics of Medical Imaging},
	volume = {9412},
	year = {2015},
	pages = {941214},
	publisher = {SPIE},
	organization = {SPIE},
	address = {Orlando, Florida, United States},
	doi = {10.1117/12.2082979},
	url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.2082979},
	author = {Das, Mini and Kandel, Bigyan and Park, Chan Soo and Zhihua Liang},
	editor = {Hoeschen, Christoph and Kontos, Despina and Flohr, Thomas G.}
}
@inproceedings {2044,
	title = {SPIE ProceedingsSingle-step, quantitative x-ray differential phase contrast imaging using spectral detection in a coded aperture setup},
	booktitle = {SPIE Medical ImagingMedical Imaging 2015: Physics of Medical Imaging},
	volume = {9412},
	year = {2015},
	pages = {941252},
	publisher = {SPIE},
	organization = {SPIE},
	address = {Orlando, Florida, United States},
	doi = {10.1117/12.2082977},
	url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.2082977},
	author = {Das, Mini and Zhihua Liang},
	editor = {Hoeschen, Christoph and Kontos, Despina and Flohr, Thomas G.}
}
@article {forde2015structural,
	title = {Structural brain network analysis in families multiply affected with bipolar I disorder},
	journal = {Psychiatry Research: Neuroimaging},
	volume = {234},
	number = {1},
	year = {2015},
	pages = {44{\textendash}51},
	publisher = {Elsevier},
	author = {Forde, Natalie J and O{\textquoteright}Donoghue, Stefani and Scanlon, Cathy and Louise Emsell and Chaddock, Chris and Alexander Leemans and Ben Jeurissen and Gareth J. Barker and Dara M. Cannon and Murray, Robin M and others}
}
@conference {1554,
	title = {Structural brain network analysis in families multiply affected with bipolar 1 disorder},
	year = {2014},
	address = {Athens, Greece},
	author = {Forde, Natalie J and Scanlon, Cathy and Louise Emsell and O{\textquoteright}Donoghue, S and Chaddock, Chris and Alexander Leemans and Ben Jeurissen and Dara M. Cannon and Murray, R M and Colm McDonald}
}
@article {1546,
	title = {Structural neuroimaging correlates of allelic variation of the BDNF val66met polymorphism.},
	journal = {NeuroImage},
	volume = {90},
	year = {2014},
	month = {2014 Apr 15},
	pages = {280-9},
	abstract = {BACKGROUND: The brain-derived neurotrophic factor (BDNF) val66met polymorphism is associated with altered activity dependent secretion of BDNF and a variable influence on brain morphology and cognition. Although a met-dose effect is generally assumed, to date the paucity of met-homozygotes have limited our understanding of the role of the met-allele on brain structure.

METHODS: To investigate this phenomenon, we recruited sixty normal healthy subjects, twenty in each genotypic group (val/val, val/met and met/met). Global and local morphology were assessed using voxel based morphometry and surface reconstruction methods. White matter organisation was also investigated using tract-based spatial statistics and constrained spherical deconvolution tractography.

RESULTS: Morphological analysis revealed an "inverted-U" shaped profile of cortical changes, with val/met heterozygotes most different relative to the two homozygous groups. These results were evident at a global and local level as well as in tractography analysis of white matter fibre bundles.

CONCLUSION: In contrast to our expectations, we found no evidence of a linear met-dose effect on brain structure, rather our results support the view that the heterozygotic BDNF val66met genotype is associated with cortical morphology that is more distinct from the BDNF val66met homozygotes. These results may prove significant in furthering our understanding of the role of the BDNF met-allele in disorders such as Alzheimer{\textquoteright}s disease and depression.},
	keywords = {Adolescent, Adult, Alleles, Brain, Brain-Derived Neurotrophic Factor, diffusion tensor imaging, Female, Genotype, Heterozygote, Homozygote, Humans, Image Processing, Computer-Assisted, Male, Middle Aged, Polymorphism, Single Nucleotide, Young Adult},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2013.12.050},
	author = {Forde, Natalie J and Ronan, Lisa and Suckling, John and Scanlon, Cathy and Neary, Simon and Holleran, Laurena and Alexander Leemans and Tait, Roger and Rua, Catarina and Fletcher, Paul C and Ben Jeurissen and Dodds, Chris M and Miller, Sam R and Bullmore, Edward T and Colm McDonald and Nathan, Pradeep J and Dara M. Cannon}
}
@inproceedings {1422,
	title = {Practical Error Bounds for Binary Tomography},
	booktitle = {1st International Conference on Tomography of Materials and Structures},
	year = {2013},
	pages = {97-100},
	author = {Wagner Fortes and Jan Sijbers and Kees Joost Batenburg}
}
@article {1515,
	title = {Extraction of airways from CT (EXACT{\textquoteright}09).},
	journal = {IEEE Transactions on Medical Imaging},
	volume = {31},
	year = {2012},
	month = {2012 Nov},
	pages = {2093-107},
	abstract = {This paper describes a framework for establishing a reference airway tree segmentation, which was used to quantitatively evaluate fifteen different airway tree extraction algorithms in a standardized manner. Because of the sheer difficulty involved in manually constructing a complete reference standard from scratch, we propose to construct the reference using results from all algorithms that are to be evaluated. We start by subdividing each segmented airway tree into its individual branch segments. Each branch segment is then visually scored by trained observers to determine whether or not it is a correctly segmented part of the airway tree. Finally, the reference airway trees are constructed by taking the union of all correctly extracted branch segments. Fifteen airway tree extraction algorithms from different research groups are evaluated on a diverse set of twenty chest computed tomography (CT) scans of subjects ranging from healthy volunteers to patients with severe pathologies, scanned at different sites, with different CT scanner brands, models, and scanning protocols. Three performance measures covering different aspects of segmentation quality were computed for all participating algorithms. Results from the evaluation showed that no single algorithm could extract more than an average of 74\% of the total length of all branches in the reference standard, indicating substantial differences between the algorithms. A fusion scheme that obtained superior results is presented, demonstrating that there is complementary information provided by the different algorithms and there is still room for further improvements in airway segmentation algorithms.},
	keywords = {Algorithms, Analysis of Variance, Databases, Factual, Humans, Lung, Radiographic Image Enhancement, Tomography, X-Ray Computed, Trachea},
	issn = {1558-254X},
	doi = {10.1109/TMI.2012.2209674},
	author = {Lo, Pechin and van Ginneken, Bram and Reinhardt, Joseph M and Yavarna, Tarunashree and de Jong, Pim A and Irving, Benjamin and Fetita, Catalin and Ortner, Margarete and R{\^o}mulo Pinho and Jan Sijbers and Feuerstein, Marco and Fabija{\'n}ska, Anna and Bauer, Christian and Beichel, Reinhard and Mendoza, Carlos S and Wiemker, Rafael and Lee, Jaesung and Reeves, Anthony P and Born, Silvia and Weinheimer, Oliver and van Rikxoort, Eva M and Tschirren, Juerg and Mori, Ken and Odry, Benjamin and Naidich, David P and Hartmann, Ieneke and Eric A. Hoffman and Prokop, Mathias and Pedersen, Jesper H and de Bruijne, Marleen}
}
@conference {M.J.bjeurissP.J.K.J.aleemans2011,
	title = {Fiber architecture of the female pelvic floor: An exploratory investigation using different diffusion MRI tractography algorithms},
	year = {2011},
	month = {May},
	address = {Montreal, Canada},
	author = {Martijn Froeling and Strijkers G. J. and Ben Jeurissen and van der Paardt M. P. and J. Stoker and K. Nicolay and A. J. Nederveen and Alexander Leemans}
}
@article {P.M.A.S.bjeurissJ.A.M.K.F.T.J.-F.C.2011,
	title = {Quantitative Evaluation of 10 Tractography Algorithms on a Realistic Diffusion MR Phantom},
	journal = {NeuroImage},
	volume = {56},
	number = {1},
	year = {2011},
	month = {May},
	pages = {220-234},
	author = {Pierre Fillard and Maxime Descoteaux and Alvina Goh and Sylvain Gouttard and Ben Jeurissen and James Malcolm and Alonso Ramirez-Manzanares and Marco Reisert and Ken Sakaie and Fatima Tensaouti and Ting-Shou Yo and Jean-Fran{\c c}ois Mangin and Cyril Poupon}
}
@conference {1553,
	title = {White Matter Tract Deficits in Schizophrenia},
	volume = {7},
	year = {2011},
	address = {Dublin, Ireland},
	author = {Forde, Natalie J and Ellison-Wright, I and Nathan, Pradeep J and Zaman, R and Dudas, R and Agius, M and Fernandez-Egea, E and Alexander Leemans and Ben Jeurissen and Scanlon, Cathy and Colm McDonald and Dara M. Cannon}
}
@conference {bjeurissaleemansefieremajsijbers2008,
	title = {Fiber Tractography on a Crossing Fiber Phantom using Constrained Spherical Deconvolution MRI},
	year = {2008},
	address = {Li{\`e}ge, Belgium},
	author = {Ben Jeurissen and Alexander Leemans and Els Fieremans and Jan Sijbers}
}
@article {asmolderMartinoStaerenpscheundjsijbersGoebelFormisano2007,
	title = {Dissecting cognitive stages with time-resolved fMRI data: a comparison of fuzzy clustering and independent component analysis},
	journal = {Magnetic Resonance Imaging},
	volume = {25},
	number = {6},
	year = {2007},
	month = {July},
	pages = {860-868},
	doi = {doi:10.1016/j.mri.2007.02.018},
	author = {Alain Smolders and F. De Martino and N. Staeren and Paul Scheunders and Jan Sijbers and R. Goebel and E. Formisano}
}
@inproceedings {gvgompelDefrisedvandyck2006,
	title = {Elliptical Extrapolation of Truncated 2D CT Projections using Helgason-Ludwig consistency conditions},
	booktitle = {SPIE Medical Imaging: Physics of Medical Imaging},
	series = {Proceedings of the SPIE},
	volume = {6142},
	year = {2006},
	month = {February},
	pages = {1408-1417},
	address = {San Diego, Californa, USA},
	author = {Gert Van Gompel and M. Defrise and Dirk Van Dyck},
	editor = {Flynn, Michael J.; Hsieh, Jiang.}
}
@inproceedings {DelputtealeemansFieremansDeeneDAsselerLemahieuAchtenjsijbersWalle2005,
	title = {Density Regularized Fiber Tractography of the Brain White Matter using Diffusion Tensor MRI},
	booktitle = {13th Scientific Meeting - International Society for Magnetic Resonance in Medicine},
	year = {2005},
	pages = {1309},
	address = {Miami, USA},
	author = {S. Delputte and Alexander Leemans and Els Fieremans and Y. De Deene and Y. D{\textquoteright}Asseler and I. Lemahieu and Eric Achten and Jan Sijbers and R. Van de Walle}
}
@inproceedings {mverhoyejsijbersFransenKooySorianoWillemsavdlinde1999,
	title = {In vivo neuro MRI microscopy of L1 knockout mice demonstrated similarities with human crash syndrome},
	booktitle = {Belgian Society for Neuroscience},
	year = {1999},
	month = {May},
	address = {Brussels},
	author = {Marleen Verhoye and Jan Sijbers and Erik Fransen and R.F. Kooy and P. Soriano and P. J. Willems and Annemie Van Der Linden}
}
@inproceedings {mverhoyejsijbersKooyReyniersFransenOostraWillemsavdlinde1998,
	title = {In vivo assessment of cerebellum volume in transgenic Fragile X Knockout mice using MRI microscopy at 7T},
	booktitle = {Proceedings of the International Society for Magnetic Resonance in Medicine},
	year = {1998},
	month = {April},
	address = {Sydney, Australia},
	author = {Marleen Verhoye and Jan Sijbers and R.F. Kooy and E. Reyniers and Erik Fransen and B. A. Oostra and P. J. Willems and Annemie Van Der Linden}
}
@inproceedings {mverhoyejsijbersFransenKooySorianoWillemsavdlinde1998,
	title = {In vivo neuro MRI micrsocopy of L1 Knockout mice demonstrated similarities with human CRASH syndrome},
	booktitle = {Sixth Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine},
	number = {1371},
	year = {1998},
	month = {April},
	address = {Sydney, Australia},
	author = {Marleen Verhoye and Jan Sijbers and Erik Fransen and R.F. Kooy and P. Soriano and P. J. Willems and Annemie Van Der Linden}
}
@article {FransenDhoogheCampmverhoyejsijbersReyniersSorianoKamiguchiWillemsenKoekoekZeeuwDeynavdlindeLemmonKooyWillems1998,
	title = {L1 knockout mice show dilated ventricles, vermis hypoplasia and impaired exploration patterns},
	journal = {Human Molecular Genetics},
	volume = {7},
	number = {6},
	year = {1998},
	pages = {999-1009},
	doi = {10.1093/hmg/7.6.999},
	author = {Erik Fransen and R. Dhooghe and G. Van Camp and Marleen Verhoye and Jan Sijbers and E. Reyniers and P. Soriano and H. Kamiguchi and R. Willemsen and K.E. Koekoek and C.I. De Zeeuw and P.P. De Deyn and Annemie Van Der Linden and V. Lemmon and R.F. Kooy and P. J. Willems}
}
@inproceedings {mverhoyejsijbersKooyReyniersFransenOostraWillemsavdlinde1998,
	title = {MRI as a tool to study brain structure from mouse models of mental retardation},
	booktitle = {Proceedings of SPIE Medical Imaging},
	volume = {3337},
	year = {1998},
	month = {February},
	pages = {314-320},
	address = {San Diego, CA, USA},
	author = {Marleen Verhoye and Jan Sijbers and R.F. Kooy and E. Reyniers and Erik Fransen and B. A. Oostra and P. J. Willems and Annemie Van Der Linden},
	editor = {Eric A. Hoffman}
}
@inproceedings {KooyReyniersmverhoyejsijbersFransenCampCrasOostraavdlindeWillems1997,
	title = {MRI as a tool to study brain structure from mouse models of mental retardation},
	booktitle = {Abstracts of the 8th international workshop on Fragile X syndrome and X-linked mental retardation},
	year = {1997},
	month = {August},
	address = {Picton, Ontario, Canada},
	author = {R.F. Kooy and E. Reyniers and Marleen Verhoye and Jan Sijbers and Erik Fransen and C. Van Camp and P. Cras and B. A. Oostra and Annemie Van Der Linden and P. J. Willems}
}
