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2018


Nanoscale robotic agents in biological fluids and tissues
Nanoscale robotic agents in biological fluids and tissues

Palagi, S., Walker, D. Q. T., Fischer, P.

In The Encyclopedia of Medical Robotics, 2, pages: 19-42, 2, (Editors: Desai, J. P. and Ferreira, A.), World Scientific, October 2018 (inbook)

Abstract
Nanorobots are untethered structures of sub-micron size that can be controlled in a non-trivial way. Such nanoscale robotic agents are envisioned to revolutionize medicine by enabling minimally invasive diagnostic and therapeutic procedures. To be useful, nanorobots must be operated in complex biological fluids and tissues, which are often difficult to penetrate. In this chapter, we first discuss potential medical applications of motile nanorobots. We briefly present the challenges related to swimming at such small scales and we survey the rheological properties of some biological fluids and tissues. We then review recent experimental results in the development of nanorobots and in particular their design, fabrication, actuation, and propulsion in complex biological fluids and tissues. Recent work shows that their nanoscale dimension is a clear asset for operation in biological tissues, since many biological tissues consist of networks of macromolecules that prevent the passage of larger micron-scale structures, but contain dynamic pores through which nanorobots can move.

pf

link (url) DOI [BibTex]

2018


link (url) DOI [BibTex]


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Instrumentation, Data, and Algorithms for Visually Understanding Haptic Surface Properties

Burka, A. L.

University of Pennsylvania, Philadelphia, USA, August 2018, Department of Electrical and Systems Engineering (phdthesis)

Abstract
Autonomous robots need to efficiently walk over varied surfaces and grasp diverse objects. We hypothesize that the association between how such surfaces look and how they physically feel during contact can be learned from a database of matched haptic and visual data recorded from various end-effectors' interactions with hundreds of real-world surfaces. Testing this hypothesis required the creation of a new multimodal sensing apparatus, the collection of a large multimodal dataset, and development of a machine-learning pipeline. This thesis begins by describing the design and construction of the Portable Robotic Optical/Tactile ObservatioN PACKage (PROTONPACK, or Proton for short), an untethered handheld sensing device that emulates the capabilities of the human senses of vision and touch. Its sensory modalities include RGBD vision, egomotion, contact force, and contact vibration. Three interchangeable end-effectors (a steel tooling ball, an OptoForce three-axis force sensor, and a SynTouch BioTac artificial fingertip) allow for different material properties at the contact point and provide additional tactile data. We then detail the calibration process for the motion and force sensing systems, as well as several proof-of-concept surface discrimination experiments that demonstrate the reliability of the device and the utility of the data it collects. This thesis then presents a large-scale dataset of multimodal surface interaction recordings, including 357 unique surfaces such as furniture, fabrics, outdoor fixtures, and items from several private and public material sample collections. Each surface was touched with one, two, or three end-effectors, comprising approximately one minute per end-effector of tapping and dragging at various forces and speeds. We hope that the larger community of robotics researchers will find broad applications for the published dataset. Lastly, we demonstrate an algorithm that learns to estimate haptic surface properties given visual input. Surfaces were rated on hardness, roughness, stickiness, and temperature by the human experimenter and by a pool of purely visual observers. Then we trained an algorithm to perform the same task as well as infer quantitative properties calculated from the haptic data. Overall, the task of predicting haptic properties from vision alone proved difficult for both humans and computers, but a hybrid algorithm using a deep neural network and a support vector machine achieved a correlation between expected and actual regression output between approximately ρ = 0.3 and ρ = 0.5 on previously unseen surfaces.

hi

Project Page [BibTex]

Project Page [BibTex]


Robust Visual Augmented Reality in Robot-Assisted Surgery
Robust Visual Augmented Reality in Robot-Assisted Surgery

Forte, M. P.

Politecnico di Milano, Milan, Italy, July 2018, Department of Electronic, Information, and Biomedical Engineering (mastersthesis)

Abstract
The broader research objective of this line of research is to test the hypothesis that real-time stereo video analysis and augmented reality can increase safety and task efficiency in robot-assisted surgery. This master’s thesis aims to solve the first step needed to achieve this goal: the creation of a robust system that delivers the envisioned feedback to a surgeon while he or she controls a surgical robot that is identical to those used on human patients. Several approaches for applying augmented reality to da Vinci Surgical Systems have been proposed, but none of them entirely rely on a clinical robot; specifically, they require additional sensors, depend on access to the da Vinci API, are designed for a very specific task, or were tested on systems that are starkly different from those in clinical use. There has also been prior work that presents the real-world camera view and the computer graphics on separate screens, or not in real time. In other scenarios, the digital information is overlaid manually by the surgeons themselves or by computer scientists, rather than being generated automatically in response to the surgeon’s actions. We attempted to overcome the aforementioned constraints by acquiring input signals from the da Vinci stereo endoscope and providing augmented reality to the console in real time (less than 150 ms delay, including the 62 ms of inherent latency of the da Vinci). The potential benefits of the resulting system are broad because it was built to be general, rather than customized for any specific task. The entire platform is compatible with any generation of the da Vinci System and does not require a dVRK (da Vinci Research Kit) or access to the API. Thus, it can be applied to existing da Vinci Systems in operating rooms around the world.

hi

Project Page [BibTex]

Project Page [BibTex]


Colloidal Chemical Nanomotors
Colloidal Chemical Nanomotors

Alarcon-Correa, M.

Colloidal Chemical Nanomotors, pages: 150, Cuvillier Verlag, MPI-IS , June 2018 (phdthesis)

Abstract
Synthetic sophisticated nanostructures represent a fundamental building block for the development of nanotechnology. The fabrication of nanoparticles complex in structure and material composition is key to build nanomachines that can operate as man-made nanoscale motors, which autonomously convert external energy into motion. To achieve this, asymmetric nanoparticles were fabricated combining a physical vapor deposition technique known as NanoGLAD and wet chemical synthesis. This thesis primarily concerns three complex colloidal systems that have been developed: i)Hollow nanocup inclusion complexes that have a single Au nanoparticle in their pocket. The Au particle can be released with an external trigger. ii)The smallest self-propelling nanocolloids that have been made to date, which give rise to a local concentration gradient that causes enhanced diffusion of the particles. iii)Enzyme-powered pumps that have been assembled using bacteriophages as biological nanoscaffolds. This construct also can be used for enzyme recovery after heterogeneous catalysis.

pf

[BibTex]

[BibTex]


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Haptics and Haptic Interfaces

Kuchenbecker, K. J.

In Encyclopedia of Robotics, (Editors: Marcelo H. Ang and Oussama Khatib and Bruno Siciliano), Springer, May 2018 (incollection)

Abstract
Haptics is an interdisciplinary field that seeks to both understand and engineer touch-based interaction. Although a wide range of systems and applications are being investigated, haptics researchers often concentrate on perception and manipulation through the human hand. A haptic interface is a mechatronic system that modulates the physical interaction between a human and his or her tangible surroundings. Haptic interfaces typically involve mechanical, electrical, and computational layers that work together to sense user motions or forces, quickly process these inputs with other information, and physically respond by actuating elements of the user’s surroundings, thereby enabling him or her to act on and feel a remote and/or virtual environment.

hi

link (url) DOI [BibTex]

link (url) DOI [BibTex]


Impact of Trunk Orientation  for Dynamic Bipedal Locomotion
Impact of Trunk Orientation for Dynamic Bipedal Locomotion

Drama, O.

Dynamic Walking Conference, May 2018 (talk)

Abstract
Impact of trunk orientation for dynamic bipedal locomotion My research revolves around investigating the functional demands of bipedal running, with focus on stabilizing trunk orientation. When we think about postural stability, there are two critical questions we need to answer: What are the necessary and sufficient conditions to achieve and maintain trunk stability? I am concentrating on how morphology affects control strategies in achieving trunk stability. In particular, I denote the trunk pitch as the predominant morphology parameter and explore the requirements it imposes on a chosen control strategy. To analyze this, I use a spring loaded inverted pendulum model extended with a rigid trunk, which is actuated by a hip motor. The challenge for the controller design here is to have a single hip actuator to achieve two coupled tasks of moving the legs to generate motion and stabilizing the trunk. I enforce orthograde and pronograde postures and aim to identify the effect of these trunk orientations on the hip torque and ground reaction profiles for different control strategies.

dlg

Impact of trunk orientation for dynamic bipedal locomotion [DW 2018] link (url) Project Page [BibTex]


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Poster Abstract: Toward Fast Closed-loop Control over Multi-hop Low-power Wireless Networks

Mager, F., Baumann, D., Trimpe, S., Zimmerling, M.

Proceedings of the 17th ACM/IEEE Conference on Information Processing in Sensor Networks (IPSN), pages: 158-159, Porto, Portugal, April 2018 (poster)

ics

DOI Project Page [BibTex]

DOI Project Page [BibTex]


Model-based Optical Flow: Layers, Learning, and Geometry
Model-based Optical Flow: Layers, Learning, and Geometry

Wulff, J.

Tuebingen University, April 2018 (phdthesis)

Abstract
The estimation of motion in video sequences establishes temporal correspondences between pixels and surfaces and allows reasoning about a scene using multiple frames. Despite being a focus of research for over three decades, computing motion, or optical flow, remains challenging due to a number of difficulties, including the treatment of motion discontinuities and occluded regions, and the integration of information from more than two frames. One reason for these issues is that most optical flow algorithms only reason about the motion of pixels on the image plane, while not taking the image formation pipeline or the 3D structure of the world into account. One approach to address this uses layered models, which represent the occlusion structure of a scene and provide an approximation to the geometry. The goal of this dissertation is to show ways to inject additional knowledge about the scene into layered methods, making them more robust, faster, and more accurate. First, this thesis demonstrates the modeling power of layers using the example of motion blur in videos, which is caused by fast motion relative to the exposure time of the camera. Layers segment the scene into regions that move coherently while preserving their occlusion relationships. The motion of each layer therefore directly determines its motion blur. At the same time, the layered model captures complex blur overlap effects at motion discontinuities. Using layers, we can thus formulate a generative model for blurred video sequences, and use this model to simultaneously deblur a video and compute accurate optical flow for highly dynamic scenes containing motion blur. Next, we consider the representation of the motion within layers. Since, in a layered model, important motion discontinuities are captured by the segmentation into layers, the flow within each layer varies smoothly and can be approximated using a low dimensional subspace. We show how this subspace can be learned from training data using principal component analysis (PCA), and that flow estimation using this subspace is computationally efficient. The combination of the layered model and the low-dimensional subspace gives the best of both worlds, sharp motion discontinuities from the layers and computational efficiency from the subspace. Lastly, we show how layered methods can be dramatically improved using simple semantics. Instead of treating all layers equally, a semantic segmentation divides the scene into its static parts and moving objects. Static parts of the scene constitute a large majority of what is shown in typical video sequences; yet, in such regions optical flow is fully constrained by the depth structure of the scene and the camera motion. After segmenting out moving objects, we consider only static regions, and explicitly reason about the structure of the scene and the camera motion, yielding much better optical flow estimates. Furthermore, computing the structure of the scene allows to better combine information from multiple frames, resulting in high accuracies even in occluded regions. For moving regions, we compute the flow using a generic optical flow method, and combine it with the flow computed for the static regions to obtain a full optical flow field. By combining layered models of the scene with reasoning about the dynamic behavior of the real, three-dimensional world, the methods presented herein push the envelope of optical flow computation in terms of robustness, speed, and accuracy, giving state-of-the-art results on benchmarks and pointing to important future research directions for the estimation of motion in natural scenes.

ps

Official link DOI Project Page [BibTex]


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Representation of sensory uncertainty in macaque visual cortex

Goris, R., Henaff, O., Meding, K.

Computational and Systems Neuroscience (COSYNE) 2018, March 2018 (poster)

ei

[BibTex]

[BibTex]


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A virtual reality environment for experiments in assistive robotics and neural interfaces

Bustamante, S.

Graduate School of Neural Information Processing, Eberhard Karls Universität Tübingen, Germany, 2018 (mastersthesis)

ei

PDF [BibTex]

PDF [BibTex]


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Optimal Trajectory Generation and Learning Control for Robot Table Tennis

Koc, O.

Technical University Darmstadt, Germany, 2018 (phdthesis)

ei

[BibTex]

[BibTex]


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Distribution-Dissimilarities in Machine Learning

Simon-Gabriel, C. J.

Eberhard Karls Universität Tübingen, Germany, 2018 (phdthesis)

ei

[BibTex]

[BibTex]


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Generalized phase locking analysis of electrophysiology data

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

7th AREADNE Conference on Research in Encoding and Decoding of Neural Ensembles, 2018 (poster)

ei

link (url) Project Page [BibTex]

link (url) Project Page [BibTex]


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Domain Adaptation Under Causal Assumptions

Lechner, T.

Eberhard Karls Universität Tübingen, Germany, 2018 (mastersthesis)

ei

[BibTex]

[BibTex]


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A Causal Perspective on Deep Representation Learning

Suter, R.

ETH Zurich, 2018 (mastersthesis)

ei

[BibTex]


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Maschinelles Lernen: Entwicklung ohne Grenzen?

Schökopf, B.

In Mit Optimismus in die Zukunft schauen. Künstliche Intelligenz - Chancen und Rahmenbedingungen, pages: 26-34, (Editors: Bender, G. and Herbrich, R. and Siebenhaar, K.), B&S Siebenhaar Verlag, 2018 (incollection)

ei

[BibTex]

[BibTex]


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Probabilistic Approaches to Stochastic Optimization

Mahsereci, M.

Eberhard Karls Universität Tübingen, Germany, 2018 (phdthesis)

ei pn

link (url) Project Page [BibTex]

link (url) Project Page [BibTex]


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Reinforcement Learning for High-Speed Robotics with Muscular Actuation

Guist, S.

Ruprecht-Karls-Universität Heidelberg , 2018 (mastersthesis)

ei

[BibTex]

[BibTex]


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Methods in Psychophysics

Wichmann, F. A., Jäkel, F.

In Stevens’ Handbook of Experimental Psychology and Cognitive Neuroscience, 5 (Methodology), 7, 4th, John Wiley & Sons, Inc., 2018 (inbook)

ei

[BibTex]

[BibTex]


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Photorealistic Video Super Resolution

Pérez-Pellitero, E., Sajjadi, M. S. M., Hirsch, M., Schölkopf, B.

Workshop and Challenge on Perceptual Image Restoration and Manipulation (PIRM) at the 15th European Conference on Computer Vision (ECCV), 2018 (poster)

ei

[BibTex]

[BibTex]


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Retinal image quality of the human eye across the visual field

Meding, K., Hirsch, M., Wichmann, F. A.

14th Biannual Conference of the German Society for Cognitive Science (KOGWIS 2018), 2018 (poster)

ei

[BibTex]

[BibTex]


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Transfer Learning for BCIs

Jayaram, V., Fiebig, K., Peters, J., Grosse-Wentrup, M.

In Brain–Computer Interfaces Handbook, pages: 425-442, 22, (Editors: Chang S. Nam, Anton Nijholt and Fabien Lotte), CRC Press, 2018 (incollection)

ei

Project Page [BibTex]

Project Page [BibTex]


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Probabilistic Ordinary Differential Equation Solvers — Theory and Applications

Schober, M.

Eberhard Karls Universität Tübingen, Germany, 2018 (phdthesis)

ei pn

[BibTex]

[BibTex]


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A machine learning approach to taking EEG-based computer interfaces out of the lab

Jayaram, V.

Graduate Training Centre of Neuroscience, IMPRS, Eberhard Karls Universität Tübingen, Germany, 2018 (phdthesis)

ei

[BibTex]

[BibTex]


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XMCD investigations on new hard magnetic systems

Chen, Y.

Universität Stuttgart, Stuttgart, 2018 (phdthesis)

mms

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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High-Resolution X-ray Ptychography for Magnetic Imaging

Bykova, I.

Universität Stuttgart, Stuttgart, 2018 (phdthesis)

mms

link (url) DOI [BibTex]

link (url) DOI [BibTex]

2011


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Projected Newton-type methods in machine learning

Schmidt, M., Kim, D., Sra, S.

In Optimization for Machine Learning, pages: 305-330, (Editors: Sra, S., Nowozin, S. and Wright, S. J.), MIT Press, Cambridge, MA, USA, December 2011 (inbook)

Abstract
We consider projected Newton-type methods for solving large-scale optimization problems arising in machine learning and related fields. We first introduce an algorithmic framework for projected Newton-type methods by reviewing a canonical projected (quasi-)Newton method. This method, while conceptually pleasing, has a high computation cost per iteration. Thus, we discuss two variants that are more scalable, namely, two-metric projection and inexact projection methods. Finally, we show how to apply the Newton-type framework to handle non-smooth objectives. Examples are provided throughout the chapter to illustrate machine learning applications of our framework.

ei

PDF Web [BibTex]

2011


PDF Web [BibTex]


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Combined whole-body PET/MR imaging: MR contrast agents do not affect the quantitative accuracy of PET following attenuation correction

Lois, C., Kupferschläger, J., Bezrukov, I., Schmidt, H., Werner, M., Mannheim, J., Pichler, B., Schwenzer, N., Beyer, T.

(SST15-05 ), 97th Scientific Assemble and Annual Meeting of the Radiological Society of North America (RSNA), December 2011 (talk)

Abstract
PURPOSE Combined PET/MR imaging entails the use of MR contrast agents (MRCA) as part of integrated protocols. We assess additional attenuation of the PET emission signals in the presence of oral and intraveneous (iv) MRCA made up of iron oxide and Gd-chelates, respectively. METHOD AND MATERIALS Phantom scans were performed on a clinical PET/CT (Biograph HiRez16, Siemens) and integrated whole-body PET/MR (Biograph mMR, Siemens) using oral (Lumirem) and intraveneous (Gadovist) MRCA. Reference PET attenuation values were determined on a small-animal PET (Inveon, Siemens) using standard PET transmission imaging (TX). Seven syringes of 5mL were filled with (a) Water, (b) Lumirem_100 (100% conc.), (c) Gadovist_100 (100%), (d) Gadovist_18 (18%), (e) Gadovist_02 (0.2%), (f) Imeron-400 CT iv-contrast (100%) and (g) Imeron-400 (2.4%). The same set of syringes was scanned on CT (Sensation16, Siemens) at 120kVp and 160mAs. The effect of MRCA on the attenuation of PET emission data was evaluated using a 20cm cylinder filled uniformly with [18F]-FDG (FDG) in water (BGD). Three 4.5cm diameter cylinders were inserted into the phantom: (C1) Teflon, (C2) Water+FDG (2:1) and (C3) Lumirem_100+FDG (2:1). Two 50mL syringes filled with Gadovist_02+FDG (Sy1) and water+FDG (Sy2) were attached to the sides of (C1) to mimick the effects of iv-contrast in vessels near bone. Syringe-to-background activity ratio was 4-to-1. PET emission data were acquired for 10min each using the PET/CT and the PET/MR. Images were reconstructed using CT- and MR-based attenuation correction. RESULTS Mean linear PET attenuation (cm-1) on TX was (a) 0.098, (b) 0.098, (c) 0.300, (d) 0.134, (e) 0.095, (f) 0.397 and (g) 0.105. Corresponding CT attenuation (HU) was: (a) 5, (b) 14, (c) 3070, (d) 1040, (e) 13, (f) 3070 and (g) 347. Lumirem had little effect on PET attenuation with (C3) being 13% and 10% higher than (C2) on PET/CT and PET/MR, respectively. Gadovist_02 had even smaller effects with (Sy1) being 2.5% lower than (Sy2) on PET/CT and 1.2% higher than (Sy2) on PET/MR. CONCLUSION MRCA in high and clinically relevant concentrations have attenuation values similar to that of CT contrast and water, respectively. In clinical PET/MR scenarios MRCA are not expected to lead to significant attenuation of the PET emission signals.

ei

Web [BibTex]

Web [BibTex]


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Spatiotemporal mapping of rhythmic activity in the inferior convexity of the macaque prefrontal cortex

Panagiotaropoulos, T., Besserve, M., Crocker, B., Kapoor, V., Tolias, A., Panzeri, S., Logothetis, N.

41(239.15), 41st Annual Meeting of the Society for Neuroscience (Neuroscience), November 2011 (poster)

Abstract
The inferior convexity of the macaque prefrontal cortex (icPFC) is known to be involved in higher order processing of sensory information mediating stimulus selection, attention and working memory. Until now, the vast majority of electrophysiological investigations of the icPFC employed single electrode recordings. As a result, relatively little is known about the spatiotemporal structure of neuronal activity in this cortical area. Here we study in detail the spatiotemporal properties of local field potentials (LFP's) in the icPFC using multi electrode recordings during anesthesia. We computed the LFP-LFP coherence as a function of frequency for thousands of pairs of simultaneously recorded sites anterior to the arcuate and inferior to the principal sulcus. We observed two distinct peaks of coherent oscillatory activity between approximately 4-10 and 15-25 Hz. We then quantified the instantaneous phase of these frequency bands using the Hilbert transform and found robust phase gradients across recording sites. The dependency of the phase on the spatial location reflects the existence of traveling waves of electrical activity in the icPFC. The dominant axis of these traveling waves roughly followed the ventral-dorsal plane. Preliminary results show that repeated visual stimulation with a 10s movie had no dramatic effect on the spatial structure of the traveling waves. Traveling waves of electrical activity in the icPFC could reflect highly organized cortical processing in this area of prefrontal cortex.

ei

Web [BibTex]

Web [BibTex]


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Cooperative Cuts: a new use of submodularity in image segmentation

Jegelka, S.

Second I.S.T. Austria Symposium on Computer Vision and Machine Learning, October 2011 (talk)

ei

Web [BibTex]

Web [BibTex]


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Effect of MR Contrast Agents on Quantitative Accuracy of PET in Combined Whole-Body PET/MR Imaging

Lois, C., Bezrukov, I., Schmidt, H., Schwenzer, N., Werner, M., Pichler, B., Kupferschläger, J., Beyer, T.

2011(MIC3-3), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (talk)

Abstract
Combined whole-body PET/MR systems are being tested in clinical practice today. Integrated imaging protocols entail the use of MR contrast agents (MRCA) that could bias PET attenuation correction. In this work, we assess the effect of MRCA in PET/MR imaging. We analyze the effect of oral and intravenous MRCA on PET activity after attenuation correction. We conclude that in clinical scenarios, MRCA are not expected to lead to significant attenuation of PET signals, and that attenuation maps are not biased after the ingestion of adequate oral contrasts.

ei

Web [BibTex]

Web [BibTex]


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First Results on Patients and Phantoms of a Fully Integrated Clinical Whole-Body PET/MRI

Schmidt, H., Schwenzer, N., Bezrukov, I., Kolb, A., Mantlik, F., Kupferschläger, J., Lois, C., Sauter, A., Brendle, C., Pfannenberg, C., Pichler, B.

2011(J2-8), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (talk)

Abstract
First clinical fully integrated whole-body PET/MR scanners are just entering the field. Here, we present studies toward quantification accuracy and variation within the PET field of view of small lesions from our BrainPET/MRI, a dedicated clinical brain scanner which was installed three years ago in Tbingen. Also, we present first results for patient and phantom scans of a fully integral whole-body PET/MRI, which was installed two months ago at our department. The quantification accuracy and homogeneity of the BrainPET-Insert (Siemens Medical Solutions, Germany) installed inside the magnet bore of a clinical 3T MRI scanner (Magnetom TIM Trio, Siemens Medical Solutions, Germany) was evaluated by using eight hollow spheres with inner diameters from 3.95 to 7.86 mm placed at different positions inside a homogeneous cylinder phantom with an 9:1 and 6:1 sphere to background ratio. The quantification accuracy for small lesions at different positions in the PET FoV shows a standard deviation of up to 11% and is acceptable for quantitative brain studies where the homogeneity of quantification on the entire FoV is essental. Image quality and resolution of the new Siemens whole-body PET/MR system (Biograph mMR, Siemens Medical Solutions, Germany) was evaluated according to the NEMA NU2 2007 protocol using a body phantom containing six spheres with inner diameter from 10 to 37 mm at sphere to background ratios of 8:1 and 4:1 and the F-18 point sources located at different positions inside the PET FoV, respectively. The evaluation of the whole-body PET/MR system reveals a good PET image quality and resolution comparable to state-of-the-art clinical PET/CT scanners. First images of patient studies carried out at the whole-body PET/MR are presented highlighting the potency of combined PET/MR imaging.

ei

Web [BibTex]

Web [BibTex]


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Evaluation and Optimization of MR-Based Attenuation Correction Methods in Combined Brain PET/MR

Mantlik, F., Hofmann, M., Bezrukov, I., Schmidt, H., Kolb, A., Beyer, T., Reimold, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-96), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
Combined PET/MR provides simultaneous molecular and functional information in an anatomical context with unique soft tissue contrast. However, PET/MR does not support direct derivation of attenuation maps of objects and tissues within the measured PET field-of-view. Valid attenuation maps are required for quantitative PET imaging, specifically for scientific brain studies. Therefore, several methods have been proposed for MR-based attenuation correction (MR-AC). Last year, we performed an evaluation of different MR-AC methods, including simple MR thresholding, atlas- and machine learning-based MR-AC. CT-based AC served as gold standard reference. RoIs from 2 anatomic brain atlases with different levels of detail were used for evaluation of correction accuracy. We now extend our evaluation of different MR-AC methods by using an enlarged dataset of 23 patients from the integrated BrainPET/MR (Siemens Healthcare). Further, we analyze options for improving the MR-AC performance in terms of speed and accuracy. Finally, we assess the impact of ignoring BrainPET positioning aids during the course of MR-AC. This extended study confirms the overall prediction accuracy evaluation results of the first evaluation in a larger patient population. Removing datasets affected by metal artifacts from the Atlas-Patch database helped to improve prediction accuracy, although the size of the database was reduced by one half. Significant improvement in prediction speed can be gained at a cost of only slightly reduced accuracy, while further optimizations are still possible.

ei

Web [BibTex]

Web [BibTex]


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Atlas- and Pattern Recognition Based Attenuation Correction on Simultaneous Whole-Body PET/MR

Bezrukov, I., Schmidt, H., Mantlik, F., Schwenzer, N., Hofmann, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-116), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
With the recent availability of clinical whole-body PET/MRI it is possible to evaluate and further develop MR-based attenuation correction methods using simultaneously acquired PET/MR data. We present first results for MRAC on patient data acquired on a fully integrated whole-body PET/MRI (Biograph mMR, Siemens) using our method that applies atlas registration and pattern recognition (ATPR) and compare them to the segmentation-based (SEG) method provided by the manufacturer. The ATPR method makes use of a database of previously aligned pairs of MR-CT volumes to predict attenuation values on a continuous scale. The robustness of the method in presence of MR artifacts was improved by location and size based detection. Lesion to liver and lesion to blood ratios (LLR and LBR) were compared for both methods on 29 iso-contour ROIs in 4 patients. ATPR showed >20% higher LBR and LLR for ROIs in and >7% near osseous tissue. For ROIs in soft tissue, both methods yielded similar ratios with max. differences <6% . For ROIs located within metal artifacts in the MR image, ATPR showed >190% higher LLR and LBR than SEG, where ratios <0.1 occured. For lesions in the neighborhood of artifacts, both ratios were >15% higher for ATPR. If artifacts in MR volumes caused by metal implants are not accounted for in the computation of attenuation maps, they can lead to a strong decrease of lesion to background ratios, even to disappearance of hot spots. Metal implants are likely to occur in the patient collective receiving combined PET/MR scans, of our first 10 patients, 3 had metal implants. Our method is currently able to account for artifacts in the pelvis caused by prostheses. The ability of the ATPR method to account for bone leads to a significant increase of LLR and LBR in osseous tissue, which supports our previous evaluations with combined PET/CT and PET/MR data. For lesions within soft tissue, lesion to background ratios of ATPR and SEG were comparable.

ei

Web [BibTex]

Web [BibTex]


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Retrospective blind motion correction of MR images

Loktyushin, A., Nickisch, H., Pohmann, R.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):498, 28th Annual Scientific Meeting ESMRMB, October 2011 (poster)

Abstract
We present a retrospective method, which significantly reduces ghosting and blurring artifacts due to subject motion. No modifications to the sequence (as in [2, 3]), or the use of additional equipment (as in [1]) are required. Our method iteratively searches for the transformation, that applied to the lines in k-space -- yields the sparsest Laplacian filter output in the spatial domain.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Model based reconstruction for GRE EPI

Blecher, W., Pohmann, R., Schölkopf, B., Seeger, M.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):493-494, 28th Annual Scientific Meeting ESMRMB, October 2011 (poster)

Abstract
Model based nonlinear image reconstruction methods for MRI [3] are at the heart of modern reconstruction techniques (e.g.compressed sensing [6]). In general, models are expressed as a matrix equation where y and u are column vectors of k-space and image data, X model matrix and e independent noise. However, solving the corresponding linear system is not tractable. Therefore fast nonlinear algorithms that minimize a function wrt.the unknown image are the method of choice: In this work a model for gradient echo EPI, is proposed that incorporates N/2 Ghost correction and correction for field inhomogeneities. In addition to reconstruction from full data, the model allows for sparse reconstruction, joint estimation of image, field-, and relaxation-map (like [5,8] for spiral imaging), and improved N/2 ghost correction.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Effect of MR contrast agents on quantitative accuracy of PET in combined whole-body PET/MR imaging

Lois, C., Kupferschläger, J., Bezrukov, I., Schmidt, H., Werner, M., Mannheim, J., Pichler, B., Schwenzer, N., Beyer, T.

(OP314), Annual Congress of the European Association of Nuclear Medicine (EANM), October 2011 (talk)

Abstract
PURPOSE:Combined PET/MR imaging entails the use of MR contrast agents (MRCA) as part of integrated protocols. MRCA are made up of iron oxide and Gd-chelates for oral and intravenous (iv) application, respectively. We assess additional attenuation of the PET emission signals in the presence of oral and iv MRCA.MATERIALS AND METHODS:Phantom scans were performed on a clinical PET/CT (Biograph HiRez16, Siemens) and an integrated whole-body PET/MR (Biograph mMR, Siemens). Two common MRCA were evaluated: Lumirem (oral) and Gadovist (iv).Reference PET attenuation values were determined on a dedicated small-animal PET (Inveon, Siemens) using equivalent standard PET transmission source imaging (TX). Seven syringes of 5mL were filled with (a) Water, (b) Lumirem_100 (100% concentration), (c) Gadovist_100 (100%), (d) Gadovist_18 (18%), (e) Gadovist_02 (0.2%), (f) Imeron-400 CT iv-contrast (100%) and (g) Imeron-400 (2.4%). The same set of syringes was scanned on CT (Sensation16, Siemens) at 120kVp and 160mAs.The effect of MRCA on the attenuation of PET emission data was evaluated using a 20cm cylinder filled uniformly with [18F]-FDG (FDG) in water (BGD). Three 4.5cm diameter cylinders were inserted into the phantom: (C1) Teflon, (C2) Water+FDG (2:1) and (C3) Lumirem_100+FDG (2:1). Two 50mL syringes filled with Gadovist_02+FDG (Sy1) and water+FDG (Sy2) were attached to the sides of (C1) to mimick the effects of iv-contrast in vessels near bone. Syringe-to-background activity ratio was 4-to-1.PET emission data were acquired for 10min each using the PET/CT and the PET/MR. Images were reconstructed using CT- and MR-based attenuation correction (AC). Since Teflon is not correctly identified on MR, PET(/MR) data were reconstructed using MR-AC and CT-AC.RESULTS:Mean linear PET attenuation (cm-1) on TX was (a) 0.098, (b) 0.098, (c) 0.300, (d) 0.134, (e) 0.095, (f) 0.397 and (g) 0.105. Corresponding CT attenuation (HU) was: (a) 5, (b) 14, (c) 3070, (d) 1040, (e) 13, (f) 3070 and (g) 347.Lumirem had little effect on PET attenuation with (C3) being 13%, 10% and 11% higher than (C2) on PET/CT, PET/MR with MR-AC, and PET/MR with CT-AC, respectively. Gadovist_02 had even smaller effects with (Sy1) being 2.5% lower, 1.2% higher, and 3.5% lower than (Sy2) on PET/CT, PET/MR with MR-AC and PET/MR with CT-AC, respectively.CONCLUSION:MRCA in high and clinically relevant concentrations have attenuation values similar to that of CT contrast and water, respectively. In clinical PET/MR scenarios MRCA are not expected to lead to significant attenuation of the PET emission signals.

ei

Web [BibTex]

Web [BibTex]


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Simultaneous multimodal imaging of patients with bronchial carcinoma in a whole body MR/PET system

Brendle, C., Sauter, A., Schmidt, H., Schraml, C., Bezrukov, I., Martirosian, P., Hetzel, J., Müller, M., Claussen, C., Schwenzer, N., Pfannenberg, C.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):141, 28th annual scientific meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRB), October 2011 (poster)

Abstract
Purpose/Introduction: Lung cancer is among the most frequent cancers (1). Exact determination of tumour extent and viability is crucial for adequate therapy guidance. [18F]-FDG-PET allows accurate staging and the evaluation of therapy response based on glucose metabolism. Diffusion weighted MRI (DWI) is another promising tool for the evaluation of tumour viability (2,3). The aim of the study was the simultaneous PET-MR acquisition in lung cancer patients and correlation of PET and MR data. Subjects and Methods: Seven patients (age 38-73 years, mean 61 years) with highly suspected or known bronchial carcinoma were examined. First, a [18F]-FDG-PET/CT was performed (injected dose: 332-380 MBq). Subsequently, patients were examined at the whole-body MR/PET (Siemens Biograph mMR). The MRI is a modified 3T Verio whole body system with a magnet bore of 60 cm (max. amplitude gradients 45 mT/m, max. slew rate 200 T/m/s). Concerning the PET, the whole-body MR/PET system comprises 56 detector cassettes with a 59.4 cm transaxial and 25.8 cm axial FoV. The following parameters for PET acquisition were applied: 2 bed positions, 6 min/bed with an average uptake time of 124 min after injection (range: 110-143 min). The attenuation correction of PET data was conducted with a segmentation-based method provided by the manufacturer. Acquired PET data were reconstructed with an iterative 3D OSEM algorithm using 3 iterations and 21 subsets, Gaussian filter of 3 mm. DWI MR images were recorded simultaneously for each bed using two b-values (0/800 s/mm2). SUVmax and ADCmin were assessed in a ROI analysis. The following ratios were calculated: SUVmax(tumor)/SUVmean(liver) and ADCmin(tumor)/ADCmean(muscle). Correlation between SUV and ADC was analyzed (Pearson’s correlation). Results: Diagnostic scans could be obtained in all patients with good tumour delineation. The spatial matching of PET and DWI data was very exact. Most tumours showed a pronounced FDG-uptake in combination with decreased ADC values. Significant correlation was found between SUV and ADC ratios (r = -0.87, p = 0.0118). Discussion/Conclusion: Simultaneous MR/PET imaging of lung cancer is feasible. The whole-body MR/PET system can provide complementary information regarding tumour viability and cellularity which could facilitate a more profound tumour characterization. Further studies have to be done to evaluate the importance of these parameters for therapy decisions and monitoring

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Multi-parametric Tumor Characterization and Therapy Monitoring using Simultaneous PET/MRI: initial results for Lung Cancer and GvHD

Sauter, A., Schmidt, H., Gueckel, B., Brendle, C., Bezrukov, I., Mantlik, F., Kolb, A., Mueller, M., Reimold, M., Federmann, B., Hetzel, J., Claussen, C., Pfannenberg, C., Horger, M., Pichler, B., Schwenzer, N.

(T110), 2011 World Molecular Imaging Congress (WMIC), September 2011 (talk)

Abstract
Hybrid imaging modalities such as [18F]FDG-PET/CT are superior in staging of e.g. lung cancer disease compared with stand-alone modalities. Clinical PET/MRI systems are about to enter the field of hybrid imaging and offer potential advantages. One added value could be a deeper insight into the tumor metabolism and tumorigenesis due to the combination of PET and dedicated MR methods such as MRS and DWI. Additionally, therapy monitoring of diffucult to diagnose disease such as chronic sclerodermic GvHD (csGvHD) can potentially be improved by this combination. We have applied PET/MRI in 3 patients with lung cancer and 4 patients with csGvHD before and during therapy. All 3 patients had lung cancer confirmed by histology (2 adenocarcinoma, 1 carcinoid). First, a [18F]FDG-PET/CT was performed with the following parameters: injected dose 351.7±25.1 MBq, uptake time 59.0±2.6 min, 3 min/bed. Subsequently, patients were brought to the PET/MRI imaging facility. The whole-body PET/MRI Biograph mMR system comprises 56 detector cassettes with a 59.4 cm transaxial and 25.8 cm axial FoV. The MRI is a modified Verio system with a magnet bore of 60 cm. The following parameters for PET acquisition were applied: uptake time 121.3±2.3 min, 3 bed positions, 6 min/bed. T1w, T2w, and DWI MR images were recorded simultaneously for each bed. Acquired PET data were reconstructed with an iterative 3D OSEM algorithm using 3 iterations and 21 subsets, Gaussian filter of 3 mm. The 4 patients with GvHD were brought to the brainPET/MRI imaging facility 2:10h-2:28h after tracer injection. A 9 min brainPET-acquisition with simultaneous MRI of the lower extremities was accomplished. MRI examination included T1-weighted (pre and post gadolinium) and T2-weighted sequences. Attenuation correction was calculated based on manual bone segmentation and thresholds for soft tissue, fat and air. Soleus muscle (m), crural fascia (f1) and posterior crural intermuscular septum fascia (f2) were surrounded with ROIs based on the pre-treatment T1-weighted images and coregistered using IRW (Siemens). Fascia-to-muscle ratios for PET (f/m), T1 contrast uptake (T1_post-contrast_f-pre-contrast_f/post-contrast_m-pre-contrast_m) and T2 (T2_f/m) were calculated. Both patients with adenocarcinoma show a lower ADC value compared with the carcinoid patient suggesting a higher cellularity. This is also reflected in FDG-PET with higher SUV values. Our initial results reveal that PET/MRI can provide complementary information for a profound tumor characterization and therapy monitoring. The high soft tissue contrast provided by MRI is valuable for the assessment of the fascial inflammation. While in the first patient FDG and contrast uptake as well as edema, represented by T2 signals, decreased with ongoing therapy, all parameters remained comparatively stable in the second patient. Contrary to expectations, an increase in FDG uptake of patient 3 and 4 was accompanied by an increase of the T2 signals, but a decrease in contrast uptake. These initial results suggest that PET/MRI provides complementary information of the complex disease mechanisms in fibrosing disorders.

ei

Web [BibTex]

Web [BibTex]


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Statistical Image Analysis and Percolation Theory

Langovoy, M., Habeck, M., Schölkopf, B.

2011 Joint Statistical Meetings (JSM), August 2011 (talk)

Abstract
We develop a novel method for detection of signals and reconstruction of images in the presence of random noise. The method uses results from percolation theory. We specifically address the problem of detection of multiple objects of unknown shapes in the case of nonparametric noise. The noise density is unknown and can be heavy-tailed. The objects of interest have unknown varying intensities. No boundary shape constraints are imposed on the objects, only a set of weak bulk conditions is required. We view the object detection problem as hypothesis testing for discrete statistical inverse problems. We present an algorithm that allows to detect greyscale objects of various shapes in noisy images. We prove results on consistency and algorithmic complexity of our procedures. Applications to cryo-electron microscopy are presented.

ei

Web [BibTex]

Web [BibTex]


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Statistical Learning Theory: Models, Concepts, and Results

von Luxburg, U., Schölkopf, B.

In Handbook of the History of Logic, Vol. 10: Inductive Logic, 10, pages: 651-706, (Editors: Gabbay, D. M., Hartmann, S. and Woods, J. H.), Elsevier North Holland, Amsterdam, Netherlands, May 2011 (inbook)

Abstract
Statistical learning theory provides the theoretical basis for many of today's machine learning algorithms and is arguably one of the most beautifully developed branches of artificial intelligence in general. It originated in Russia in the 1960s and gained wide popularity in the 1990s following the development of the so-called Support Vector Machine (SVM), which has become a standard tool for pattern recognition in a variety of domains ranging from computer vision to computational biology. Providing the basis of new learning algorithms, however, was not the only motivation for developing statistical learning theory. It was just as much a philosophical one, attempting to answer the question of what it is that allows us to draw valid conclusions from empirical data. In this article we attempt to give a gentle, non-technical overview over the key ideas and insights of statistical learning theory. We do not assume that the reader has a deep background in mathematics, statistics, or computer science. Given the nature of the subject matter, however, some familiarity with mathematical concepts and notations and some intuitive understanding of basic probability is required. There exist many excellent references to more technical surveys of the mathematics of statistical learning theory: the monographs by one of the founders of statistical learning theory ([Vapnik, 1995], [Vapnik, 1998]), a brief overview over statistical learning theory in Section 5 of [Sch{\"o}lkopf and Smola, 2002], more technical overview papers such as [Bousquet et al., 2003], [Mendelson, 2003], [Boucheron et al., 2005], [Herbrich and Williamson, 2002], and the monograph [Devroye et al., 1996].

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Crowdsourcing for optimisation of deconvolution methods via an iPhone application

Lang, A.

Hochschule Reutlingen, Germany, April 2011 (mastersthesis)

ei

[BibTex]

[BibTex]


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Cooperative Cuts

Jegelka, S.

COSA Workshop: Combinatorial Optimization, Statistics, and Applications, March 2011 (talk)

Abstract
Combinatorial problems with submodular cost functions have recently drawn interest. In a standard combinatorial problem, the sum-of-weights cost is replaced by a submodular set function. The result is a powerful model that is though very hard. In this talk, I will introduce cooperative cuts, minimum cuts with submodular edge weights. I will outline methods to approximately solve this problem, and show an application in computer vision. If time permits, the talk will also sketch regret-minimizing online algorithms for submodular-cost combinatorial problems. This is joint work with Jeff Bilmes (University of Washington).

ei

Web [BibTex]

Web [BibTex]


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Robot Learning

Peters, J., Tedrake, R., Roy, N., Morimoto, J.

In Encyclopedia of Machine Learning, pages: 865-869, Encyclopedia of machine learning, (Editors: Sammut, C. and Webb, G. I.), Springer, New York, NY, USA, January 2011 (inbook)

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Support Vector Machines for finding deletions and short insertions using paired-end short reads

Grimm, D., Hagmann, J., König, D., Weigel, D., Borgwardt, KM.

International Conference on Intelligent Systems for Molecular Biology (ISMB), 2011 (poster)

ei

Web [BibTex]

Web [BibTex]


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What You Expect Is What You Get? Potential Use of Contingent Negative Variation for Passive BCI Systems in Gaze-Based HCI

Ihme, K., Zander, TO.

In Affective Computing and Intelligent Interaction, 6975, pages: 447-456, Lecture Notes in Computer Science, (Editors: D’Mello, S., Graesser, A., Schuller, B. and Martin, J.-C.), Springer, Berlin, Germany, 2011 (inbook)

Abstract
When using eye movements for cursor control in human-computer interaction (HCI), it may be difficult to find an appropriate substitute for the click operation. Most approaches make use of dwell times. However, in this context the so-called Midas-Touch-Problem occurs which means that the system wrongly interprets fixations due to long processing times or spontaneous dwellings of the user as command. Lately it has been shown that brain-computer interface (BCI) input bears good prospects to overcome this problem using imagined hand movements to elicit a selection. The current approach tries to develop this idea further by exploring potential signals for the use in a passive BCI, which would have the advantage that the brain signals used as input are generated automatically without conscious effort of the user. To explore event-related potentials (ERPs) giving information about the user’s intention to select an object, 32-channel electroencephalography (EEG) was recorded from ten participants interacting with a dwell-time-based system. Comparing ERP signals during the dwell time with those occurring during fixations on a neutral cross hair, a sustained negative slow cortical potential at central electrode sites was revealed. This negativity might be a contingent negative variation (CNV) reflecting the participants’ anticipation of the upcoming selection. Offline classification suggests that the CNV is detectable in single trial (mean accuracy 74.9 %). In future, research on the CNV should be accomplished to ensure its stable occurence in human-computer interaction and render possible its use as a potential substitue for the click operation.

ei

DOI [BibTex]

DOI [BibTex]