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The costs and benefits of estimating T₁ of tissue alongside cerebral blood flow and arterial transit time in pseudo-continuous arterial spin labeling

Bladt, Piet (author), den Dekker, A.J. (author), Clement, Patricia (author), Achten, Eric (author), Sijbers, Jan (author)

Multi-post-labeling-delay pseudo-continuous arterial spin labeling (multi-PLD PCASL) allows for absolute quantification of the cerebral blood flow (CBF) as well as the arterial transit time (ATT). Estimating these perfusion parameters from multi-PLD PCASL data is a non-linear inverse problem, which is commonly tackled by fitting the single...

journal article 2019

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Diffusion Kurtosis Imaging with free water elimination: A Bayesian estimation approach

Collier, Quinten (author), Veraart, Jelle (author), Jeurissen, Ben (author), Vanhevel, Floris (author), Pullens, Pim (author), Parizel, Paul M. (author), den Dekker, A.J. (author), Sijbers, JJM (author)

Purpose: Diffusion kurtosis imaging (DKI) is an advanced magnetic resonance imaging modality that is known to be sensitive to changes in the underlying microstructure of the brain. Image voxels in diffusion weighted images, however, are typically relatively large making them susceptible to partial volume effects, especially when part of the...

journal article 2018

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Single atom detection from low contrast-to-noise ratio electron microscopy images

Fatermans, J. (author), den Dekker, A.J. (author), Müller-Caspary, K. (author), Lobato, I. (author), O’Leary, C.M. (author), Nellist, P.D. (author), Van Aert, S. (author)

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...

journal article 2018

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Parametric reconstruction of glass fiber-reinforced polymer composites from X-ray projection data—A simulation study

Elberfeld, Tim (author), De Beenhouwer, Jan (author), den Dekker, A.J. (author), Heinzl, Christoph (author), Sijbers, Jan (author)

We present a new approach to estimate geometry parameters of glass fibers in glass fiber-reinforced polymers from simulated X-ray micro-computed tomography scans. Traditionally, these parameters are estimated using a multi-step procedure including image reconstruction, pre-processing, segmentation and analysis of features of interest. Each...

journal article 2018

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A nonlocal maximum likelihood estimation method for enhancing magnetic resonance phase maps

Sudeep, P. V. (author), Palanisamy, P. (author), Kesavadas, Chandrasekharan (author), Sijbers, JJM (author), den Dekker, A.J. (author), Rajan, Jeny (author)

A phase map can be obtained from the real and imaginary components of a complex valued magnetic resonance (MR) image. Many applications, such as MR phase velocity mapping and susceptibility mapping, make use of the information contained in the MR phase maps. Unfortunately, noise in the complex MR signal affects the measurement of parameters...

journal article 2017

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A unified Maximum Likelihood framework for simultaneous motion and T1 estimation in quantitative MR T1 mapping

Ramos-Llorden, Gabriel (author), den Dekker, A.J. (author), Van Steenkiste, Gwendolyn Van (author), Jeurissen, Ben (author), Vanhevel, Floris (author), Audekerke, Johan Van (author), Verhoye, Marleen (author), Sijbers, Jan (author)

In quantitative MR T1 mapping, the spin-lattice relaxation time T1 of tissues is estimated from a series of T1-weighted images. As the T1 estimation is a voxel-wise estimation procedure, correct spatial alignment of the T1-weighted images is crucial. Conventionally, the T1-weighted images are first registered based on a general-purpose...

journal article 2017

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Partial discreteness: A novel prior for magnetic resonance image reconstruction

Ramos-Llorden, Gabriel (author), den Dekker, A.J. (author), Sijbers, Jan (author)

An important factor influencing the quality of magnetic resonance (MR) images is the reconstruction method that is employed, and specifically, the type of prior knowledge that is exploited during reconstruction. In this work, we introduce a new type of prior knowledge, partial discreteness (PD), where a small number of regions in the image...

journal article 2017

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Atom-counting in High Resolution Electron Microscopy: TEM or STEM – That's the question

Gonnissen, J. (author), De Backer, A. (author), den Dekker, A.J. (author), Sijbers, J. (author), Van Aert, S. (author)

In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the...

journal article 2017

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Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design

Gonnissen, J. (author), De Backer, A. (author), den Dekker, A.J. (author), Sijbers, J. (author), Van Aert, S. (author)

In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the...

journal article 2016

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Advanced electron crystallography through model-based imaging

Van Aert, Sandra (author), De Backer, Annick (author), Martinez, Gerardo T. (author), den Dekker, A.J. (author), Van Dyck, Dirk (author), Bals, Sara (author), Van Tendeloo, Gustaaf (author)

The increasing need for precise determination of the atomic arrangement of non-periodic structures in materials design and the control of nanostructures explains the growing interest in quantitative transmission electron microscopy. The aim is to extract precise and accurate numbers for unknown structure parameters including atomic positions,...

journal article 2016

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Multi-voxel algorithm for quantitative bi-exponential MRI T₁ estimation

Bladt, P. (author), Van Steenkiste, G. (author), Ramos-Llordén, G. (author), den Dekker, A.J. (author), Sijbers, J. (author)

Quantification of the spin-lattice relaxation time, T₁, of tissues is important for characterization of tissues in clinical magnetic resonance imaging (MRI). In T₁ mapping, T₁ values are estimated from a set of T₁-weighted MRI images. Due to the limited spatial resolution of the T₁...

conference paper 2016

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Optimal experimental design for the detection of light atoms from high-resolution scanning transmission electron microscopy images

Gonnissen, J. (author), De Backer, A. (author), Den Dekker, A.J. (author), Martinez, G.T. (author), Rosenauer, A. (author), Sijbers, J. (author), Van Aert, S. (author)

We report an innovative method to explore the optimal experimental settings to detect light atoms from scanning transmission electron microscopy (STEM) images. Since light elements play a key role in many technologically important materials, such as lithium-battery devices or hydrogen storage applications, much effort has been made to optimize...

journal article 2014

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Iterative linear focal-plane wavefront correction

Smith, C.S. (author), Marinica, R.M. (author), Den Dekker, A.J. (author), Verhaegen, M.H.G. (author), Korkiakoski, V. (author), Keller, C.U. (author), Doelman, N. (author)

We propose an efficient approximation to the nonlinear phase diversity (PD) method for wavefront reconstruction and correction from intensity measurements with potential of being used in real-time applications. The new iterative linear phase diversity (ILPD) method assumes that the residual phase aberration is small and makes use of a first...

journal article 2013

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Electron microscope and method of estimating defocus therefor

Tejada Ruiz, A. (author), Den Dekker, A.J. (author)

patent 2012

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Estimation of Diffusion Properties in Crossing Fiber Bundles

Caan, M.W.A. (author), Ganesh Khedoe, H. (author), Poot, D.H.J. (author), Den Dekker, A.J. (author), Olabarriaga, S.D. (author), Grimbergen, K.A. (author), Van Vliet, L.J. (author), Vos, F.M. (author)

There is an ongoing debate on how to model diffusivity in fiber crossings. We propose an optimization framework for the selection of a dual tensor model and the set of diffusion weighting parameters b, such that both the diffusion shape and orientation parameters can be precisely as well as accurately estimated. For that, we have adopted the...

journal article 2010

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Observer Development for Automatic STEM Closed-Loop Control

Tejada, A. (author), Den Dekker, A.J. (author), Van der Hoeven, S.W. (author)

journal article 2009

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Alignment control of STEM: A Ronchigram based approach

Van der Hoeven, S.W. (author), Den dekker, A.J. (author), Tejada, A. (author)

journal article 2009

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Likelihood-Based Hypothesis Tests for Brain Activation Detection From MRI Data Disturbed by Colored Noise: A Simulation Study

Den Dekker, A.J. (author), Poot, D.H.J. (author), Bos, R. (author), Sijbers, J. (author)

Functional magnetic resonance imaging (fMRI) data that are corrupted by temporally colored noise are generally preprocessed (i.e., prewhitened or precolored) prior to functional activation detection. In this paper, we propose likelihood-based hypothesis tests that account for colored noise directly within the framework of functional activation...

journal article 2009

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Automatic estimation of the noise variance from the histogram of a magnetic resonance image

Sijbers, J. (author), Poot, D. (author), Den Dekker, A.J. (author), Pintjens, W. (author)

journal article 2007

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Resolution of coherent and incoherent imaging systems reconsidered: Classical criteria and a statistical alternative

Van Aert, S. (author), Van Dyck, D. (author), Den Dekker, A.J. (author)

The resolution of coherent and incoherent imaging systems is usually evaluated in terms of classical resolution criteria, such as Rayleigh’s. Based on these criteria, incoherent imaging is generally concluded to be ‘better’ than coherent imaging. However, this paper reveals some misconceptions in the application of the classical criteria, which...

journal article 2006