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2017


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Improving performance of linear field generation with multi-coil setup by optimizing coils position

Aghaeifar, A., Loktyushin, A., Eschelbach, M., Scheffler, K.

Magnetic Resonance Materials in Physics, Biology and Medicine, 30(Supplement 1):S259, 34th Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB), October 2017 (poster)

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link (url) DOI [BibTex]

2017


link (url) DOI [BibTex]


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Estimating B0 inhomogeneities with projection FID navigator readouts

Loktyushin, A., Ehses, P., Schölkopf, B., Scheffler, K.

25th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2017 (poster)

ei

link (url) [BibTex]

link (url) [BibTex]


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Image Quality Improvement by Applying Retrospective Motion Correction on Quantitative Susceptibility Mapping and R2*

Feng, X., Loktyushin, A., Deistung, A., Reichenbach, J.

25th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2017 (poster)

ei

link (url) [BibTex]

link (url) [BibTex]


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Elements of Causal Inference - Foundations and Learning Algorithms

Peters, J., Janzing, D., Schölkopf, B.

Adaptive Computation and Machine Learning Series, The MIT Press, Cambridge, MA, USA, 2017 (book)

ei

PDF [BibTex]

PDF [BibTex]


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Mobile Microrobotics

Sitti, M.

Mobile Microrobotics, The MIT Press, Cambridge, MA, 2017 (book)

Abstract
Progress in micro- and nano-scale science and technology has created a demand for new microsystems for high-impact applications in healthcare, biotechnology, manufacturing, and mobile sensor networks. The new robotics field of microrobotics has emerged to extend our interactions and explorations to sub-millimeter scales. This is the first textbook on micron-scale mobile robotics, introducing the fundamentals of design, analysis, fabrication, and control, and drawing on case studies of existing approaches. The book covers the scaling laws that can be used to determine the dominant forces and effects at the micron scale; models forces acting on microrobots, including surface forces, friction, and viscous drag; and describes such possible microfabrication techniques as photo-lithography, bulk micromachining, and deep reactive ion etching. It presents on-board and remote sensing methods, noting that remote sensors are currently more feasible; studies possible on-board microactuators; discusses self-propulsion methods that use self-generated local gradients and fields or biological cells in liquid environments; and describes remote microrobot actuation methods for use in limited spaces such as inside the human body. It covers possible on-board powering methods, indispensable in future medical and other applications; locomotion methods for robots on surfaces, in liquids, in air, and on fluid-air interfaces; and the challenges of microrobot localization and control, in particular multi-robot control methods for magnetic microrobots. Finally, the book addresses current and future applications, including noninvasive medical diagnosis and treatment, environmental remediation, and scientific tools.

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Mobile Microrobotics By Metin Sitti - Chapter 1 (PDF) link (url) [BibTex]

Mobile Microrobotics By Metin Sitti - Chapter 1 (PDF) link (url) [BibTex]


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New Directions for Learning with Kernels and Gaussian Processes (Dagstuhl Seminar 16481)

Gretton, A., Hennig, P., Rasmussen, C., Schölkopf, B.

Dagstuhl Reports, 6(11):142-167, 2017 (book)

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DOI [BibTex]

DOI [BibTex]


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Design of a visualization scheme for functional connectivity data of Human Brain

Bramlage, L.

Hochschule Osnabrück - University of Applied Sciences, 2017 (thesis)

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Bramlage_BSc_2017.pdf [BibTex]


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Generalized phase locking analysis of electrophysiology data

Safavi, S., Panagiotaropoulos, T., Kapoor, V., Logothetis, N. K., Besserve, M.

ESI Systems Neuroscience Conference (ESI-SyNC 2017): Principles of Structural and Functional Connectivity, 2017 (poster)

ei

[BibTex]

[BibTex]

2009


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Clinical PET/MRI-System and Its Applications with MRI Based Attenuation Correction

Kolb, A., Hofmann, M., Sossi, V., Wehrl, H., Sauter, A., Schmid, A., Schlemmer, H., Claussen, C., Pichler, B.

IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC 2009), 2009, pages: 1, October 2009 (poster)

Abstract
Clinical PET/MRI is an emerging new hybrid imaging modality. In addition to provide an unique possibility for multifunctional imaging with temporally and spatially matched data, it also provides anatomical information that can also be used for attenuation correction with no radiation exposure to the subjects. A plus of combined compared to sequential PET and MR imaging is the reduction of total scan time. Here we present our initial experience with a hybrid brain PET/MRI system. Due to the ethical approval patient scans could only be performed after a diagnostic PET/CT. We estimate that in approximately 50% of the cases PET/MRI was of superior diagnostic value compared to PET/CT and was able to provide additional information, such as DTI, spectroscopy and Time Of Flight (TOF) angiography. Here we present 3 patient cases in oncology, a retropharyngeal carcinoma in neurooncology, a relapsing meningioma and in neurology a pharyngeal carcinoma in addition to an infraction of the right hemisphere. For quantitative PET imaging attenuation correction is obligatory. In current PET/MRI setup we used our MRI based atlas method for calculating the mu-map for attenuation correction. MR-based attenuation correction accuracy was quantitatively compared to CT-based PET attenuation correction. Extensive studies to assess potential mutual interferences between PET and MR imaging modalities as well as NEMA measurements have been performed. The first patient studies as well as the phantom tests clearly demonstrated the overall good imaging performance of this first human PET/MRI system. Ongoing work concentrates on advanced normalization and reconstruction methods incorporating count-rate based algorithms.

ei

Web [BibTex]

2009


Web [BibTex]


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A flowering-time gene network model for association analysis in Arabidopsis thaliana

Klotzbücher, K., Kobayashi, Y., Shervashidze, N., Borgwardt, K., Weigel, D.

2009(39):95-96, German Conference on Bioinformatics (GCB '09), September 2009 (poster)

Abstract
In our project we want to determine a set of single nucleotide polymorphisms (SNPs), which have a major effect on the flowering time of Arabidopsis thaliana. Instead of performing a genome-wide association study on all SNPs in the genome of Arabidopsis thaliana, we examine the subset of SNPs from the flowering-time gene network model. We are interested in how the results of the association study vary when using only the ascertained subset of SNPs from the flowering network model, and when additionally using the information encoded by the structure of the network model. The network model is compiled from the literature by manual analysis and contains genes which have been found to affect the flowering time of Arabidopsis thaliana [Far+08; KW07]. The genes in this model are annotated with the SNPs that are located in these genes, or in near proximity to them. In a baseline comparison between the subset of SNPs from the graph and the set of all SNPs, we omit the structural information and calculate the correlation between the individual SNPs and the flowering time phenotype by use of statistical methods. Through this we can determine the subset of SNPs with the highest correlation to the flowering time. In order to further refine this subset, we include the additional information provided by the network structure by conducting a graph-based feature pre-selection. In the further course of this project we want to validate and examine the resulting set of SNPs and their corresponding genes with experimental methods.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Initial Data from a first PET/MRI-System and its Applications in Clinical Studies Using MRI Based Attenuation Correction

Kolb, A., Hofmann, M., Sossi, V., Wehrl, H., Sauter, A., Schmid, A., Judenhofer, M., Schlemmer, H., Claussen, C., Pichler, B.

2009 World Molecular Imaging Congress, 2009, pages: 1200, September 2009 (poster)

ei

Web [BibTex]

Web [BibTex]


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A High-Speed Object Tracker from Off-the-Shelf Components

Lampert, C., Peters, J.

First IEEE Workshop on Computer Vision for Humanoid Robots in Real Environments at ICCV 2009, 1, pages: 1, September 2009 (poster)

Abstract
We introduce RTblob, an open-source real-time vision system for 3D object detection that achieves over 200 Hz tracking speed with only off-the-shelf hardware component. It allows fast and accurate tracking of colored objects in 3D without expensive and often custom-built hardware, instead making use of the PC graphics cards for the necessary image processing operations.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Estimating Critical Stimulus Features from Psychophysical Data: The Decision-Image Technique Applied to Human Faces

Macke, J., Wichmann, F.

Journal of Vision, 9(8):31, 9th Annual Meeting of the Vision Sciences Society (VSS), August 2009 (poster)

Abstract
One of the main challenges in the sensory sciences is to identify the stimulus features on which the sensory systems base their computations: they are a pre-requisite for computational models of perception. We describe a technique---decision-images--- for extracting critical stimulus features based on logistic regression. Rather than embedding the stimuli in noise, as is done in classification image analysis, we want to infer the important features directly from physically heterogeneous stimuli. A Decision-image not only defines the critical region-of-interest within a stimulus but is a quantitative template which defines a direction in stimulus space. Decision-images thus enable the development of predictive models, as well as the generation of optimized stimuli for subsequent psychophysical investigations. Here we describe our method and apply it to data from a human face discrimination experiment. We show that decision-images are able to predict human responses not only in terms of overall percent correct but are able to predict, for individual observers, the probabilities with which individual faces are (mis-) classified. We then test the predictions of the models using optimized stimuli. Finally, we discuss possible generalizations of the approach and its relationships with other models.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Semi-supervised Analysis of Human fMRI Data

Shelton, JA., Blaschko, MB., Lampert, CH., Bartels, A.

Berlin Brain Computer Interface Workshop on Advances in Neurotechnology, 2009, pages: 1, July 2009 (poster)

Abstract
Kernel Canonical Correlation Analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, CCA learns representations tied more closely to underlying process generating the the data and can ignore high-variance noise directions. However, for data where acquisition in a given modality is expensive or otherwise limited, CCA may suffer from small sample effects. We propose to use semisupervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of CCA on human fMRI data, with regression to single and multivariate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of CCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Optimization of k-Space Trajectories by Bayesian Experimental Design

Seeger, M., Nickisch, H., Pohmann, R., Schölkopf, B.

17(2627), 17th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2009 (poster)

Abstract
MR image reconstruction from undersampled k-space can be improved by nonlinear denoising estimators since they incorporate statistical prior knowledge about image sparsity. Reconstruction quality depends crucially on the undersampling design (k-space trajectory), in a manner complicated by the nonlinear and signal-dependent characteristics of these methods. We propose an algorithm to assess and optimize k-space trajectories for sparse MRI reconstruction, based on Bayesian experimental design, which is scaled up to full MR images by a novel variational relaxation to iteratively reweighted FFT or gridding computations. Designs are built sequentially by adding phase encodes predicted to be most informative, given the combination of previous measurements with image prior information.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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MR-Based Attenuation Correction for PET/MR

Hofmann, M., Steinke, F., Bezrukov, I., Kolb, A., Aschoff, P., Lichy, M., Erb, M., Nägele, T., Brady, M., Schölkopf, B., Pichler, B.

17(260), 17th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2009 (poster)

Abstract
There has recently been a growing interest in combining PET and MR. Attenuation correction (AC), which accounts for radiation attenuation properties of the tissue, is mandatory for quantitative PET. In the case of PET/MR the attenuation map needs to be determined from the MR image. This is intrinsically difficult as MR intensities are not related to the electron density information of the attenuation map. Using ultra-short echo (UTE) acquisition, atlas registration and machine learning, we present methods that allow prediction of the attenuation map based on the MR image both for brain and whole body imaging.

ei

PDF Web [BibTex]

PDF Web [BibTex]

2002


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Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond

Schölkopf, B., Smola, A.

pages: 644, Adaptive Computation and Machine Learning, MIT Press, Cambridge, MA, USA, December 2002, Parts of this book, including an introduction to kernel methods, can be downloaded here. (book)

Abstract
In the 1990s, a new type of learning algorithm was developed, based on results from statistical learning theory: the Support Vector Machine (SVM). This gave rise to a new class of theoretically elegant learning machines that use a central concept of SVMs-kernels—for a number of learning tasks. Kernel machines provide a modular framework that can be adapted to different tasks and domains by the choice of the kernel function and the base algorithm. They are replacing neural networks in a variety of fields, including engineering, information retrieval, and bioinformatics. Learning with Kernels provides an introduction to SVMs and related kernel methods. Although the book begins with the basics, it also includes the latest research. It provides all of the concepts necessary to enable a reader equipped with some basic mathematical knowledge to enter the world of machine learning using theoretically well-founded yet easy-to-use kernel algorithms and to understand and apply the powerful algorithms that have been developed over the last few years.

ei

Web [BibTex]

2002


Web [BibTex]


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Surface-slant-from-texture discrimination: Effects of slant level and texture type

Rosas, P., Wichmann, F., Wagemans, J.

Journal of Vision, 2(7):300, Second Annual Meeting of the Vision Sciences Society (VSS), November 2002 (poster)

Abstract
The problem of surface-slant-from-texture was studied psychophysically by measuring the performances of five human subjects in a slant-discrimination task with a number of different types of textures: uniform lattices, randomly displaced lattices, polka dots, Voronoi tessellations, orthogonal sinusoidal plaid patterns, fractal or 1/f noise, “coherent” noise and a “diffusion-based” texture (leopard skin-like). The results show: (1) Improving performance with larger slants for all textures. (2) A “non-symmetrical” performance around a particular slant characterized by a psychometric function that is steeper in the direction of the more slanted orientation. (3) For sufficiently large slants (66 deg) there are no major differences in performance between any of the different textures. (4) For slants at 26, 37 and 53 degrees, however, there are marked differences between the different textures. (5) The observed differences in performance across textures for slants up to 53 degrees are systematic within subjects, and nearly so across them. This allows a rank-order of textures to be formed according to their “helpfulness” — that is, how easy the discrimination task is when a particular texture is mapped on the surface. Polka dots tended to allow the best slant discrimination performance, noise patterns the worst up to the large slant of 66 degrees at which performance was almost independent of the particular texture chosen. Finally, our large number of 2AFC trials (approximately 2800 trials per texture across subjects) and associated tight confidence intervals may enable us to find out about which statistical properties of the textures could be responsible for surface-slant-from-texture estimation, with the ultimate goal of being able to predict observer performance for any arbitrary texture.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Modelling Contrast Transfer in Spatial Vision

Wichmann, F.

Journal of Vision, 2(10):7, Second Annual Meeting of the Vision Sciences Society (VSS), November 2002 (poster)

Abstract
Much of our information about spatial vision comes from detection experiments involving low-contrast stimuli. Contrast discrimination experiments provide one way to explore the visual system's response to stimuli of higher contrast, the results of which allow different models of contrast processing (e.g. energy versus gain-control models) to be critically assessed (Wichmann & Henning, 1999). Studies of detection and discrimination using pulse train stimuli in noise, on the other hand, make predictions about the number, position and properties of noise sources within the processing stream (Henning, Bird & Wichmann, 2002). Here I report modelling results combining data from both sinusoidal and pulse train experiments in and without noise to arrive at a more tightly constrained model of early spatial vision.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Pulse train detection and discrimination in pink noise

Henning, G., Wichmann, F., Bird, C.

Journal of Vision, 2(7):229, Second Annual Meeting of the Vision Sciences Society (VSS), November 2002 (poster)

Abstract
Much of our information about spatial vision comes from detection experiments involving low-contrast stimuli. Contrast discrimination experiments provide one way to explore the visual system's response to stimuli of higher contrast. We explored both detection and contrast discrimination performance with sinusoidal and "pulse-train" (or line) gratings. Both types of grating had a fundamental spatial frequency of 2.09-c/deg but the pulse-train, ideally, contains, in addition to its fundamental component, all the harmonics of the fundamental. Although the 2.09-c/deg pulse-train produced on the display was measured and shown to contain at least 8 harmonics at equal contrast, it was no more detectable than its most detectable component; no benefit from having additional information at the harmonics was measurable. The addition of broadband "pink" noise, designed to equalize the detectability of the components of the pulse train, made it about a factor of four more detectable than any of its components. However, in contrast-discrimination experiments, with an in-phase pedestal or masking grating of the same form and phase as the signal and 15% contrast, the noise did not improve the discrimination performance of the pulse train relative to that of its sinusoidal components. In contrast, a 2.09-c/deg "super train," constructed to have 8 equally detectable harmonics, was a factor of five more detectable than any of its components. We discuss the implications of these observations for models of early vision in particular the implications for possible sources of internal noise.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Phase information in the recognition of natural images

Braun, D., Wichmann, F., Gegenfurtner, K.

Perception, 31(ECVP Abstract Supplement):133, 25th European Conference on Visual Perception, August 2002 (poster)

Abstract
Fourier phase plays an important role in determining global image structure. For example, when the phase spectrum of an image of a flower is swapped with that of a tank, we usually perceive a tank, even though the amplitude spectrum is still that of the flower. Similarly, when the phase spectrum of an image is randomly swapped across frequencies, that is its Fourier energy is randomly distributed over the image, the resulting image becomes impossible to recognise. Our goal was to evaluate the effect of phase manipulations in a quantitative manner. Subjects viewed two images of natural scenes, one of which contained an animal (the target) embedded in the background. The spectra of the images were manipulated by adding random phase noise at each frequency. The phase noise was the independent variable, uniformly distributed between 0° and ±180°. Subjects were remarkably resistant to phase noise. Even with ±120° noise, subjects were still 75% correct. The proportion of correct answers closely followed the correlation between original and noise-distorted images. Thus it appears as if it was not the global phase information per se that determines our percept of natural images, but rather the effect of phase on local image features.

ei

Web [BibTex]

Web [BibTex]


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Detection and discrimination in pink noise

Wichmann, F., Henning, G.

5, pages: 100, 5. T{\"u}binger Wahrnehmungskonferenz (TWK), February 2002 (poster)

Abstract
Much of our information about early spatial vision comes from detection experiments involving low-contrast stimuli, which are not, perhaps, particularly "natural" stimuli. Contrast discrimination experiments provide one way to explore the visual system's response to stimuli of higher contrast whilst keeping the number of unknown parameters comparatively small. We explored both detection and contrast discrimination performance with sinusoidal and "pulse-train" (or line) gratings. Both types of grating had a fundamental spatial frequency of 2.09-c/deg but the pulse-train, ideally, contains, in addition to its fundamental component, all the harmonics of the fundamental. Although the 2.09-c/deg pulse-train produced on our display was measured using a high-performance digital camera (Photometrics) and shown to contain at least 8 harmonics at equal contrast, it was no more detectable than its most detectable component; no benefit from having additional information at the harmonics was measurable. The addition of broadband 1-D "pink" noise made it about a factor of four more detectable than any of its components. However, in contrast-discrimination experiments, with an in-phase pedestal or masking grating of the same form and phase as the signal and 15% contrast, the noise did not improve the discrimination performance of the pulse train relative to that of its sinusoidal components. We discuss the implications of these observations for models of early vision in particular the implications for possible sources of internal noise.

ei

Web [BibTex]

Web [BibTex]


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Application of Monte Carlo Methods to Psychometric Function Fitting

Wichmann, F.

Proceedings of the 33rd European Conference on Mathematical Psychology, pages: 44, 2002 (poster)

Abstract
The psychometric function relates an observer's performance to an independent variable, usually some physical quantity of a stimulus in a psychophysical task. Here I describe methods to (1) fitting psychometric functions, (2) assessing goodness-of-fit, and (3) providing confidence intervals for the function's parameters and other estimates derived from them. First I describe a constrained maximum-likelihood method for parameter estimation. Using Monte-Carlo simulations I demonstrate that it is important to have a fitting method that takes stimulus-independent errors (or "lapses") into account. Second, a number of goodness-of-fit tests are introduced. Because psychophysical data sets are usually rather small I advocate the use of Monte Carlo resampling techniques that do not rely on asymptotic theory for goodness-of-fit assessment. Third, a parametric bootstrap is employed to estimate the variability of fitted parameters and derived quantities such as thresholds and slopes. I describe how the bootstrap bridging assumption, on which the validity of the procedure depends, can be tested without incurring too high a cost in computation time. Finally I describe how the methods can be extended to test hypotheses concerning the form and shape of several psychometric functions. Software describing the methods is available (http://www.bootstrap-software.com/psignifit/), as well as articles describing the methods in detail (Wichmann&Hill, Perception&Psychophysics, 2001a,b).

ei

[BibTex]

[BibTex]


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Optimal linear estimation of self-motion - a real-world test of a model of fly tangential neurons

Franz, MO.

SAB 02 Workshop, Robotics as theoretical biology, 7th meeting of the International Society for Simulation of Adaptive Behaviour (SAB), (Editors: Prescott, T.; Webb, B.), 2002 (poster)

Abstract
The tangential neurons in the fly brain are sensitive to the typical optic flow patterns generated during self-motion (see example in Fig.1). We examine whether a simplified linear model of these neurons can be used to estimate self-motion from the optic flow. We present a theory for the construction of an optimal linear estimator incorporating prior knowledge both about the distance distribution of the environment, and about the noise and self-motion statistics of the sensor. The optimal estimator is tested on a gantry carrying an omnidirectional vision sensor that can be moved along three translational and one rotational degree of freedom. The experiments indicate that the proposed approach yields accurate results for rotation estimates, independently of the current translation and scene layout. Translation estimates, however, turned out to be sensitive to simultaneous rotation and to the particular distance distribution of the scene. The gantry experiments confirm that the receptive field organization of the tangential neurons allows them, as an ensemble, to extract self-motion from the optic flow.

ei

PDF [BibTex]

PDF [BibTex]