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2014


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MoSh: Motion and Shape Capture from Sparse Markers

Loper, M. M., Mahmood, N., Black, M. J.

ACM Transactions on Graphics, (Proc. SIGGRAPH Asia), 33(6):220:1-220:13, ACM, New York, NY, USA, November 2014 (article)

Abstract
Marker-based motion capture (mocap) is widely criticized as producing lifeless animations. We argue that important information about body surface motion is present in standard marker sets but is lost in extracting a skeleton. We demonstrate a new approach called MoSh (Motion and Shape capture), that automatically extracts this detail from mocap data. MoSh estimates body shape and pose together using sparse marker data by exploiting a parametric model of the human body. In contrast to previous work, MoSh solves for the marker locations relative to the body and estimates accurate body shape directly from the markers without the use of 3D scans; this effectively turns a mocap system into an approximate body scanner. MoSh is able to capture soft tissue motions directly from markers by allowing body shape to vary over time. We evaluate the effect of different marker sets on pose and shape accuracy and propose a new sparse marker set for capturing soft-tissue motion. We illustrate MoSh by recovering body shape, pose, and soft-tissue motion from archival mocap data and using this to produce animations with subtlety and realism. We also show soft-tissue motion retargeting to new characters and show how to magnify the 3D deformations of soft tissue to create animations with appealing exaggerations.

pdf video data pdf from publisher link (url) DOI Project Page Project Page Project Page [BibTex]

2014

pdf video data pdf from publisher link (url) DOI Project Page Project Page Project Page [BibTex]


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Can I recognize my body’s weight? The influence of shape and texture on the perception of self

Piryankova, I., Stefanucci, J., Romero, J., de la Rosa, S., Black, M., Mohler, B.

ACM Transactions on Applied Perception for the Symposium on Applied Perception, 11(3):13:1-13:18, September 2014 (article)

Abstract
The goal of this research was to investigate women’s sensitivity to changes in their perceived weight by altering the body mass index (BMI) of the participants’ personalized avatars displayed on a large-screen immersive display. We created the personalized avatars with a full-body 3D scanner that records both the participants’ body geometry and texture. We altered the weight of the personalized avatars to produce changes in BMI while keeping height, arm length and inseam fixed and exploited the correlation between body geometry and anthropometric measurements encapsulated in a statistical body shape model created from thousands of body scans. In a 2x2 psychophysical experiment, we investigated the relative importance of visual cues, namely shape (own shape vs. an average female body shape with equivalent height and BMI to the participant) and texture (own photo-realistic texture or checkerboard pattern texture) on the ability to accurately perceive own current body weight (by asking them ‘Is the avatar the same weight as you?’). Our results indicate that shape (where height and BMI are fixed) had little effect on the perception of body weight. Interestingly, the participants perceived their body weight veridically when they saw their own photo-realistic texture and significantly underestimated their body weight when the avatar had a checkerboard patterned texture. The range that the participants accepted as their own current weight was approximately a 0.83 to −6.05 BMI% change tolerance range around their perceived weight. Both the shape and the texture had an effect on the reported similarity of the body parts and the whole avatar to the participant’s body. This work has implications for new measures for patients with body image disorders, as well as researchers interested in creating personalized avatars for games, training applications or virtual reality.

pdf DOI Project Page Project Page [BibTex]

pdf DOI Project Page Project Page [BibTex]


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3D to 2D bijection for spherical objects under equidistant fisheye projection

Ahmad, A., Xavier, J., Santos-Victor, J., Lima, P.

Computer Vision and Image Understanding, 125, pages: 172-183, August 2014 (article)

Abstract
The core problem addressed in this article is the 3D position detection of a spherical object of known-radius in a single image frame, obtained by a dioptric vision system consisting of only one fisheye lens camera that follows equidistant projection model. The central contribution is a bijection principle between a known-radius spherical object’s 3D world position and its 2D projected image curve, that we prove, thus establishing that for every possible 3D world position of the spherical object, there exists a unique curve on the image plane if the object is projected through a fisheye lens that follows equidistant projection model. Additionally, we present a setup for the experimental verification of the principle’s correctness. In previously published works we have applied this principle to detect and subsequently track a known-radius spherical object.

DOI [BibTex]

DOI [BibTex]


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Breathing Life into Shape: Capturing, Modeling and Animating 3D Human Breathing

Tsoli, A., Mahmood, N., Black, M. J.

ACM Transactions on Graphics, (Proc. SIGGRAPH), 33(4):52:1-52:11, ACM, New York, NY, July 2014 (article)

Abstract
Modeling how the human body deforms during breathing is important for the realistic animation of lifelike 3D avatars. We learn a model of body shape deformations due to breathing for different breathing types and provide simple animation controls to render lifelike breathing regardless of body shape. We capture and align high-resolution 3D scans of 58 human subjects. We compute deviations from each subject’s mean shape during breathing, and study the statistics of such shape changes for different genders, body shapes, and breathing types. We use the volume of the registered scans as a proxy for lung volume and learn a novel non-linear model relating volume and breathing type to 3D shape deformations and pose changes. We then augment a SCAPE body model so that body shape is determined by identity, pose, and the parameters of the breathing model. These parameters provide an intuitive interface with which animators can synthesize 3D human avatars with realistic breathing motions. We also develop a novel interface for animating breathing using a spirometer, which measures the changes in breathing volume of a “breath actor.”

pdf video link (url) DOI Project Page Project Page Project Page [BibTex]


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3D Traffic Scene Understanding from Movable Platforms

Geiger, A., Lauer, M., Wojek, C., Stiller, C., Urtasun, R.

IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 36(5):1012-1025, published, IEEE, Los Alamitos, CA, May 2014 (article)

Abstract
In this paper, we present a novel probabilistic generative model for multi-object traffic scene understanding from movable platforms which reasons jointly about the 3D scene layout as well as the location and orientation of objects in the scene. In particular, the scene topology, geometry and traffic activities are inferred from short video sequences. Inspired by the impressive driving capabilities of humans, our model does not rely on GPS, lidar or map knowledge. Instead, it takes advantage of a diverse set of visual cues in the form of vehicle tracklets, vanishing points, semantic scene labels, scene flow and occupancy grids. For each of these cues we propose likelihood functions that are integrated into a probabilistic generative model. We learn all model parameters from training data using contrastive divergence. Experiments conducted on videos of 113 representative intersections show that our approach successfully infers the correct layout in a variety of very challenging scenarios. To evaluate the importance of each feature cue, experiments using different feature combinations are conducted. Furthermore, we show how by employing context derived from the proposed method we are able to improve over the state-of-the-art in terms of object detection and object orientation estimation in challenging and cluttered urban environments.

pdf link (url) [BibTex]

pdf link (url) [BibTex]


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Adaptive Offset Correction for Intracortical Brain Computer Interfaces

Homer, M. L., Perge, J. A., Black, M. J., Harrison, M. T., Cash, S. S., Hochberg, L. R.

IEEE Transactions on Neural Systems and Rehabilitation Engineering, 22(2):239-248, March 2014 (article)

Abstract
Intracortical brain computer interfaces (iBCIs) decode intended movement from neural activity for the control of external devices such as a robotic arm. Standard approaches include a calibration phase to estimate decoding parameters. During iBCI operation, the statistical properties of the neural activity can depart from those observed during calibration, sometimes hindering a user’s ability to control the iBCI. To address this problem, we adaptively correct the offset terms within a Kalman filter decoder via penalized maximum likelihood estimation. The approach can handle rapid shifts in neural signal behavior (on the order of seconds) and requires no knowledge of the intended movement. The algorithm, called MOCA, was tested using simulated neural activity and evaluated retrospectively using data collected from two people with tetraplegia operating an iBCI. In 19 clinical research test cases, where a nonadaptive Kalman filter yielded relatively high decoding errors, MOCA significantly reduced these errors (10.6 ± 10.1\%; p < 0.05, pairwise t-test). MOCA did not significantly change the error in the remaining 23 cases where a nonadaptive Kalman filter already performed well. These results suggest that MOCA provides more robust decoding than the standard Kalman filter for iBCIs.

pdf DOI Project Page [BibTex]

pdf DOI Project Page [BibTex]


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A physically-based approach to reflection separation: from physical modeling to constrained optimization

Kong, N., Tai, Y., Shin, J. S.

IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 36(2):209-221, IEEE Computer Society, Febuary 2014 (article)

Abstract
We propose a physically-based approach to separate reflection using multiple polarized images with a background scene captured behind glass. The input consists of three polarized images, each captured from the same view point but with a different polarizer angle separated by 45 degrees. The output is the high-quality separation of the reflection and background layers from each of the input images. A main technical challenge for this problem is that the mixing coefficient for the reflection and background layers depends on the angle of incidence and the orientation of the plane of incidence, which are spatially varying over the pixels of an image. Exploiting physical properties of polarization for a double-surfaced glass medium, we propose a multiscale scheme which automatically finds the optimal separation of the reflection and background layers. Through experiments, we demonstrate that our approach can generate superior results to those of previous methods.

Publisher site [BibTex]

Publisher site [BibTex]


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Simpler, faster, more accurate melanocytic lesion segmentation through MEDS

Peruch, F., Bogo, F., Bonazza, M., Cappelleri, V., Peserico, E.

IEEE Transactions on Biomedical Engineering, 61(2):557-565, February 2014 (article)

DOI [BibTex]

DOI [BibTex]


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A freely-moving monkey treadmill model

Foster, J., Nuyujukian, P., Freifeld, O., Gao, H., Walker, R., Ryu, S., Meng, T., Murmann, B., Black, M., Shenoy, K.

J. of Neural Engineering, 11(4):046020, 2014 (article)

Abstract
Objective: Motor neuroscience and brain-machine interface (BMI) design is based on examining how the brain controls voluntary movement, typically by recording neural activity and behavior from animal models. Recording technologies used with these animal models have traditionally limited the range of behaviors that can be studied, and thus the generality of science and engineering research. We aim to design a freely-moving animal model using neural and behavioral recording technologies that do not constrain movement. Approach: We have established a freely-moving rhesus monkey model employing technology that transmits neural activity from an intracortical array using a head-mounted device and records behavior through computer vision using markerless motion capture. We demonstrate the excitability and utility of this new monkey model, including the fi rst recordings from motor cortex while rhesus monkeys walk quadrupedally on a treadmill. Main results: Using this monkey model, we show that multi-unit threshold-crossing neural activity encodes the phase of walking and that the average ring rate of the threshold crossings covaries with the speed of individual steps. On a population level, we find that neural state-space trajectories of walking at diff erent speeds have similar rotational dynamics in some dimensions that evolve at the step rate of walking, yet robustly separate by speed in other state-space dimensions. Significance: Freely-moving animal models may allow neuroscientists to examine a wider range of behaviors and can provide a flexible experimental paradigm for examining the neural mechanisms that underlie movement generation across behaviors and environments. For BMIs, freely-moving animal models have the potential to aid prosthetic design by examining how neural encoding changes with posture, environment, and other real-world context changes. Understanding this new realm of behavior in more naturalistic settings is essential for overall progress of basic motor neuroscience and for the successful translation of BMIs to people with paralysis.

pdf Supplementary DOI Project Page [BibTex]

pdf Supplementary DOI Project Page [BibTex]


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Detection and Tracking of Occluded People

Tang, S., Andriluka, M., Schiele, B.

International Journal of Computer Vision, 110, pages: 58-69, 2014 (article)

PDF [BibTex]

PDF [BibTex]


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Segmentation of Biomedical Images Using Active Contour Model with Robust Image Feature and Shape Prior

S. Y. Yeo, X. Xie, I. Sazonov, P. Nithiarasu

International Journal for Numerical Methods in Biomedical Engineering, 30(2):232- 248, 2014 (article)

Abstract
In this article, a new level set model is proposed for the segmentation of biomedical images. The image energy of the proposed model is derived from a robust image gradient feature which gives the active contour a global representation of the geometric configuration, making it more robust in dealing with image noise, weak edges, and initial configurations. Statistical shape information is incorporated using nonparametric shape density distribution, which allows the shape model to handle relatively large shape variations. The segmentation of various shapes from both synthetic and real images depict the robustness and efficiency of the proposed method.

[BibTex]

[BibTex]


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A Quantitative Analysis of Current Practices in Optical Flow Estimation and the Principles behind Them

Sun, D., Roth, S., Black, M. J.

International Journal of Computer Vision (IJCV), 106(2):115-137, 2014 (article)

Abstract
The accuracy of optical flow estimation algorithms has been improving steadily as evidenced by results on the Middlebury optical flow benchmark. The typical formulation, however, has changed little since the work of Horn and Schunck. We attempt to uncover what has made recent advances possible through a thorough analysis of how the objective function, the optimization method, and modern implementation practices influence accuracy. We discover that "classical'' flow formulations perform surprisingly well when combined with modern optimization and implementation techniques. One key implementation detail is the median filtering of intermediate flow fields during optimization. While this improves the robustness of classical methods it actually leads to higher energy solutions, meaning that these methods are not optimizing the original objective function. To understand the principles behind this phenomenon, we derive a new objective function that formalizes the median filtering heuristic. This objective function includes a non-local smoothness term that robustly integrates flow estimates over large spatial neighborhoods. By modifying this new term to include information about flow and image boundaries we develop a method that can better preserve motion details. To take advantage of the trend towards video in wide-screen format, we further introduce an asymmetric pyramid downsampling scheme that enables the estimation of longer range horizontal motions. The methods are evaluated on Middlebury, MPI Sintel, and KITTI datasets using the same parameter settings.

pdf full text code [BibTex]


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Automatic 4D Reconstruction of Patient-Specific Cardiac Mesh with 1- to-1 Vertex Correspondence from Segmented Contours Lines

C. W. Lim, Y. Su, S. Y. Yeo, G. M. Ng, V. T. Nguyen, L. Zhong, R. S. Tan, K. K. Poh, P. Chai,

PLOS ONE, 9(4), 2014 (article)

Abstract
We propose an automatic algorithm for the reconstruction of patient-specific cardiac mesh models with 1-to-1 vertex correspondence. In this framework, a series of 3D meshes depicting the endocardial surface of the heart at each time step is constructed, based on a set of border delineated magnetic resonance imaging (MRI) data of the whole cardiac cycle. The key contribution in this work involves a novel reconstruction technique to generate a 4D (i.e., spatial–temporal) model of the heart with 1-to-1 vertex mapping throughout the time frames. The reconstructed 3D model from the first time step is used as a base template model and then deformed to fit the segmented contours from the subsequent time steps. A method to determine a tree-based connectivity relationship is proposed to ensure robust mapping during mesh deformation. The novel feature is the ability to handle intra- and inter-frame 2D topology changes of the contours, which manifests as a series of merging and splitting of contours when the images are viewed either in a spatial or temporal sequence. Our algorithm has been tested on five acquisitions of cardiac MRI and can successfully reconstruct the full 4D heart model in around 30 minutes per subject. The generated 4D heart model conforms very well with the input segmented contours and the mesh element shape is of reasonably good quality. The work is important in the support of downstream computational simulation activities.

[BibTex]

[BibTex]

2011


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High-quality reflection separation using polarized images

Kong, N., Tai, Y., Shin, S. Y.

IEEE Transactions on Image Processing, 20(12):3393-3405, IEEE Signal Processing Society, December 2011 (article)

Abstract
In this paper, we deal with a problem of separating the effect of reflection from images captured behind glass. The input consists of multiple polarized images captured from the same view point but with different polarizer angles. The output is the high quality separation of the reflection layer and the background layer from the images. We formulate this problem as a constrained optimization problem and propose a framework that allows us to fully exploit the mutually exclusive image information in our input data. We test our approach on various images and demonstrate that our approach can generate good reflection separation results.

Publisher site [BibTex]

2011

Publisher site [BibTex]


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A human inspired gaze estimation system

Wulff, J., Sinha, P.

Journal of Vision, 11(11):507-507, ARVO, September 2011 (article)

Abstract
Estimating another person's gaze is a crucial skill in human social interactions. The social component is most apparent in dyadic gaze situations, in which the looker seems to look into the eyes of the observer, thereby signaling interest or a turn to speak. In a triadic situation, on the other hand, the looker's gaze is averted from the observer and directed towards another, specific target. This is mostly interpreted as a cue for joint attention, creating awareness of a predator or another point of interest. In keeping with the task's social significance, humans are very proficient at gaze estimation. Our accuracy ranges from less than one degree for dyadic settings to approximately 2.5 degrees for triadic ones. Our goal in this work is to draw inspiration from human gaze estimation mechanisms in order to create an artificial system that can approach the former's accuracy levels. Since human performance is severely impaired by both image-based degradations (Ando, 2004) and a change of facial configurations (Jenkins & Langton, 2003), the underlying principles are believed to be based both on simple image cues such as contrast/brightness distribution and on more complex geometric processing to reconstruct the actual shape of the head. By incorporating both kinds of cues in our system's design, we are able to surpass the accuracy of existing eye-tracking systems, which rely exclusively on either image-based or geometry-based cues (Yamazoe et al., 2008). A side-benefit of this combined approach is that it allows for gaze estimation despite moderate view-point changes. This is important for settings where subjects, say young children or certain kinds of patients, might not be fully cooperative to allow a careful calibration. Our model and implementation of gaze estimation opens up new experimental questions about human mechanisms while also providing a useful tool for general calibration-free, non-intrusive remote eye-tracking.

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Detecting synchrony in degraded audio-visual streams

Dhandhania, K., Wulff, J., Sinha, P.

Journal of Vision, 11(11):800-800, ARVO, September 2011 (article)

Abstract
Even 8–10 week old infants, when presented with two dynamic faces and a speech stream, look significantly longer at the ‘correct’ talking person (Patterson & Werker, 2003). This is true even though their reduced visual acuity prevents them from utilizing high spatial frequencies. Computational analyses in the field of audio/video synchrony and automatic speaker detection (e.g. Hershey & Movellan, 2000), in contrast, usually depend on high-resolution images. Therefore, the correlation mechanisms found in these computational studies are not directly applicable to the processes through which we learn to integrate the modalities of speech and vision. In this work, we investigated the correlation between speech signals and degraded video signals. We found a high correlation persisting even with high image degradation, resembling the low visual acuity of young infants. Additionally (in a fashion similar to Graf et al., 2002) we explored which parts of the face correlate with the audio in the degraded video sequences. Perfect synchrony and small offsets in the audio were used while finding the correlation, thereby detecting visual events preceding and following audio events. In order to achieve a sufficiently high temporal resolution, high-speed video sequences (500 frames per second) of talking people were used. This is a temporal resolution unachieved in previous studies and has allowed us to capture very subtle and short visual events. We believe that the results of this study might be interesting not only to vision researchers, but, by revealing subtle effects on a very fine timescale, also to people working in computer graphics and the generation and animation of artificial faces.

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Trajectory Space: A Dual Representation for Nonrigid Structure from Motion

Akhter, I., Sheikh, Y., Khan, S., Kanade, T.

Pattern Analysis and Machine Intelligence, IEEE Transactions on, 33(7):1442-1456, IEEE, July 2011 (article)

Abstract
Existing approaches to nonrigid structure from motion assume that the instantaneous 3D shape of a deforming object is a linear combination of basis shapes. These basis are object dependent and therefore have to be estimated anew for each video sequence. In contrast, we propose a dual approach to describe the evolving 3D structure in trajectory space by a linear combination of basis trajectories. We describe the dual relationship between the two approaches, showing that they both have equal power for representing 3D structure. We further show that the temporal smoothness in 3D trajectories alone can be used for recovering nonrigid structure from a moving camera. The principal advantage of expressing deforming 3D structure in trajectory space is that we can define an object independent basis. This results in a significant reduction in unknowns, and corresponding stability in estimation. We propose the use of the Discrete Cosine Transform (DCT) as the object independent basis and empirically demonstrate that it approaches Principal Component Analysis (PCA) for natural motions. We report the performance of the proposed method, quantitatively using motion capture data, and qualitatively on several video sequences exhibiting nonrigid motions including piecewise rigid motion, partially nonrigid motion (such as a facial expressions), and highly nonrigid motion (such as a person walking or dancing).

pdf project page [BibTex]

pdf project page [BibTex]


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Loose-limbed People: Estimating 3D Human Pose and Motion Using Non-parametric Belief Propagation

Sigal, L., Isard, M., Haussecker, H., Black, M. J.

International Journal of Computer Vision, 98(1):15-48, Springer Netherlands, May 2011 (article)

Abstract
We formulate the problem of 3D human pose estimation and tracking as one of inference in a graphical model. Unlike traditional kinematic tree representations, our model of the body is a collection of loosely-connected body-parts. In particular, we model the body using an undirected graphical model in which nodes correspond to parts and edges to kinematic, penetration, and temporal constraints imposed by the joints and the world. These constraints are encoded using pair-wise statistical distributions, that are learned from motion-capture training data. Human pose and motion estimation is formulated as inference in this graphical model and is solved using Particle Message Passing (PaMPas). PaMPas is a form of non-parametric belief propagation that uses a variation of particle filtering that can be applied over a general graphical model with loops. The loose-limbed model and decentralized graph structure allow us to incorporate information from "bottom-up" visual cues, such as limb and head detectors, into the inference process. These detectors enable automatic initialization and aid recovery from transient tracking failures. We illustrate the method by automatically tracking people in multi-view imagery using a set of calibrated cameras and present quantitative evaluation using the HumanEva dataset.

pdf publisher's site link (url) Project Page Project Page [BibTex]

pdf publisher's site link (url) Project Page Project Page [BibTex]


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Point-and-Click Cursor Control With an Intracortical Neural Interface System by Humans With Tetraplegia

Kim, S., Simeral, J. D., Hochberg, L. R., Donoghue, J. P., Friehs, G. M., Black, M. J.

IEEE Transactions on Neural Systems and Rehabilitation Engineering, 19(2):193-203, April 2011 (article)

Abstract
We present a point-and-click intracortical neural interface system (NIS) that enables humans with tetraplegia to volitionally move a 2D computer cursor in any desired direction on a computer screen, hold it still and click on the area of interest. This direct brain-computer interface extracts both discrete (click) and continuous (cursor velocity) signals from a single small population of neurons in human motor cortex. A key component of this system is a multi-state probabilistic decoding algorithm that simultaneously decodes neural spiking activity and outputs either a click signal or the velocity of the cursor. The algorithm combines a linear classifier, which determines whether the user is intending to click or move the cursor, with a Kalman filter that translates the neural population activity into cursor velocity. We present a paradigm for training the multi-state decoding algorithm using neural activity observed during imagined actions. Two human participants with tetraplegia (paralysis of the four limbs) performed a closed-loop radial target acquisition task using the point-and-click NIS over multiple sessions. We quantified point-and-click performance using various human-computer interaction measurements for pointing devices. We found that participants were able to control the cursor motion accurately and click on specified targets with a small error rate (< 3% in one participant). This study suggests that signals from a small ensemble of motor cortical neurons (~40) can be used for natural point-and-click 2D cursor control of a personal computer.

pdf publishers's site pub med link (url) Project Page [BibTex]

pdf publishers's site pub med link (url) Project Page [BibTex]


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A Database and Evaluation Methodology for Optical Flow

Baker, S., Scharstein, D., Lewis, J. P., Roth, S., Black, M. J., Szeliski, R.

International Journal of Computer Vision, 92(1):1-31, March 2011 (article)

Abstract
The quantitative evaluation of optical flow algorithms by Barron et al. (1994) led to significant advances in performance. The challenges for optical flow algorithms today go beyond the datasets and evaluation methods proposed in that paper. Instead, they center on problems associated with complex natural scenes, including nonrigid motion, real sensor noise, and motion discontinuities. We propose a new set of benchmarks and evaluation methods for the next generation of optical flow algorithms. To that end, we contribute four types of data to test different aspects of optical flow algorithms: (1) sequences with nonrigid motion where the ground-truth flow is determined by tracking hidden fluorescent texture, (2) realistic synthetic sequences, (3) high frame-rate video used to study interpolation error, and (4) modified stereo sequences of static scenes. In addition to the average angular error used by Barron et al., we compute the absolute flow endpoint error, measures for frame interpolation error, improved statistics, and results at motion discontinuities and in textureless regions. In October 2007, we published the performance of several well-known methods on a preliminary version of our data to establish the current state of the art. We also made the data freely available on the web at http://vision.middlebury.edu/flow/ . Subsequently a number of researchers have uploaded their results to our website and published papers using the data. A significant improvement in performance has already been achieved. In this paper we analyze the results obtained to date and draw a large number of conclusions from them.

pdf pdf from publisher Middlebury Flow Evaluation Website [BibTex]

pdf pdf from publisher Middlebury Flow Evaluation Website [BibTex]


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Neural control of cursor trajectory and click by a human with tetraplegia 1000 days after implant of an intracortical microelectrode array

(J. Neural Engineering Highlights of 2011 Collection. JNE top 10 cited papers of 2010-2011.)

Simeral, J. D., Kim, S., Black, M. J., Donoghue, J. P., Hochberg, L. R.

J. of Neural Engineering, 8(2):025027, 2011 (article)

Abstract
The ongoing pilot clinical trial of the BrainGate neural interface system aims in part to assess the feasibility of using neural activity obtained from a small-scale, chronically implanted, intracortical microelectrode array to provide control signals for a neural prosthesis system. Critical questions include how long implanted microelectrodes will record useful neural signals, how reliably those signals can be acquired and decoded, and how effectively they can be used to control various assistive technologies such as computers and robotic assistive devices, or to enable functional electrical stimulation of paralyzed muscles. Here we examined these questions by assessing neural cursor control and BrainGate system characteristics on five consecutive days 1000 days after implant of a 4 × 4 mm array of 100 microelectrodes in the motor cortex of a human with longstanding tetraplegia subsequent to a brainstem stroke. On each of five prospectively-selected days we performed time-amplitude sorting of neuronal spiking activity, trained a population-based Kalman velocity decoding filter combined with a linear discriminant click state classifier, and then assessed closed-loop point-and-click cursor control. The participant performed both an eight-target center-out task and a random target Fitts metric task which was adapted from a human-computer interaction ISO standard used to quantify performance of computer input devices. The neural interface system was further characterized by daily measurement of electrode impedances, unit waveforms and local field potentials. Across the five days, spiking signals were obtained from 41 of 96 electrodes and were successfully decoded to provide neural cursor point-and-click control with a mean task performance of 91.3% ± 0.1% (mean ± s.d.) correct target acquisition. Results across five consecutive days demonstrate that a neural interface system based on an intracortical microelectrode array can provide repeatable, accurate point-and-click control of a computer interface to an individual with tetraplegia 1000 days after implantation of this sensor.

pdf pdf from publisher link (url) Project Page [BibTex]


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Modelling pipeline for subject-specific arterial blood flow—A review

Igor Sazonov, Si Yong Yeo, Rhodri Bevan, Xianghua Xie, Raoul van Loon, Perumal Nithiarasu

International Journal for Numerical Methods in Biomedical Engineering, 27(12):1868–1910, 2011 (article)

Abstract
In this paper, a robust and semi-automatic modelling pipeline for blood flow through subject-specific arterial geometries is presented. The framework developed consists of image segmentation, domain discretization (meshing) and fluid dynamics. All the three subtopics of the pipeline are explained using an example of flow through a severely stenosed human carotid artery. In the Introduction, the state-of-the-art of both image segmentation and meshing is presented in some detail, and wherever possible the advantages and disadvantages of the existing methods are analysed. Followed by this, the deformable model used for image segmentation is presented. This model is based upon a geometrical potential force (GPF), which is a function of the image. Both the GPF calculation and level set determination are explained. Following the image segmentation method, a semi-automatic meshing method used in the present study is explained in full detail. All the relevant techniques required to generate a valid domain discretization are presented. These techniques include generating a valid surface mesh, skeletonization, mesh cropping, boundary layer mesh construction and various mesh cosmetic methods that are essential for generating a high-quality domain discretization. After presenting the mesh generation procedure, how to generate flow boundary conditions for both the inlets and outlets of a geometry is explained in detail. This is followed by a brief note on the flow solver, before studying the blood flow through the carotid artery with a severe stenosis.

[BibTex]

[BibTex]


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Geometrically Induced Force Interaction for Three-Dimensional Deformable Models

Si Yong Yeo, Xianghua Xie, Igor Sazonov, Perumal Nithiarasu

IEEE Transactions on Image Processing, 20(5):1373 - 1387, 2011 (article)

Abstract
In this paper, we propose a novel 3-D deformable model that is based upon a geometrically induced external force field which can be conveniently generalized to arbitrary dimensions. This external force field is based upon hypothesized interactions between the relative geometries of the deformable model and the object boundary characterized by image gradient. The evolution of the deformable model is solved using the level set method so that topological changes are handled automatically. The relative geometrical configurations between the deformable model and the object boundaries contribute to a dynamic vector force field that changes accordingly as the deformable model evolves. The geometrically induced dynamic interaction force has been shown to greatly improve the deformable model performance in acquiring complex geometries and highly concave boundaries, and it gives the deformable model a high invariancy in initialization configurations. The voxel interactions across the whole image domain provide a global view of the object boundary representation, giving the external force a long attraction range. The bidirectionality of the external force field allows the new deformable model to deal with arbitrary cross-boundary initializations, and facilitates the handling of weak edges and broken boundaries. In addition, we show that by enhancing the geometrical interaction field with a nonlocal edge-preserving algorithm, the new deformable model can effectively overcome image noise. We provide a comparative study on the segmentation of various geometries with different topologies from both synthetic and real images, and show that the proposed method achieves significant improvements against existing image gradient techniques.

[BibTex]

[BibTex]


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Computational flow studies in a subject-specific human upper airway using a one-equation turbulence model. Influence of the nasal cavity

Prihambodo Saksono, Perumal Nithiarasu, Igor Sazonov, Si Yong Yeo

International Journal for Numerical Methods in Biomedical Engineering, 87(1-5):96–114, 2011 (article)

Abstract
This paper focuses on the impact of including nasal cavity on airflow through a human upper respiratory tract. A computational study is carried out on a realistic geometry, reconstructed from CT scans of a subject. The geometry includes nasal cavity, pharynx, larynx, trachea and two generations of airway bifurcations below trachea. The unstructured mesh generation procedure is discussed in some length due to the complex nature of the nasal cavity structure and poor scan resolution normally available from hospitals. The fluid dynamic studies have been carried out on the geometry with and without the inclusion of the nasal cavity. The characteristic-based split scheme along with the one-equation Spalart–Allmaras turbulence model is used in its explicit form to obtain flow solutions at steady state. Results reveal that the exclusion of nasal cavity significantly influences the resulting solution. In particular, the location of recirculating flow in the trachea is dramatically different when the truncated geometry is used. In addition, we also address the differences in the solution due to imposed, equally distributed and proportionally distributed flow rates at inlets (both nares). The results show that the differences in flow pattern between the two inlet conditions are not confined to the nasal cavity and nasopharyngeal region, but they propagate down to the trachea.

[BibTex]

[BibTex]


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Predicting Articulated Human Motion from Spatial Processes

Soren Hauberg, Kim S. Pedersen

International Journal of Computer Vision, 94, pages: 317-334, Springer Netherlands, 2011 (article)

Publishers site Code Paper site PDF [BibTex]

Publishers site Code Paper site PDF [BibTex]

2007


no image
Learning static Gestalt laws through dynamic experience

Ostrovsky, Y., Wulff, J., Sinha, P.

Journal of Vision, 7(9):315-315, ARVO, June 2007 (article)

Abstract
The Gestalt laws (Wertheimer 1923) are widely regarded as the rules that help us parse the world into objects. However, it is unclear as to how these laws are acquired by an infant's visual system. Classically, these “laws” have been presumed to be innate (Kellman and Spelke 1983). But, more recent work in infant development, showing the protracted time-course over which these grouping principles emerge (e.g., Johnson and Aslin 1995; Craton 1996), suggests that visual experience might play a role in their genesis. Specifically, our studies of patients with late-onset vision (Project Prakash; VSS 2006) and evidence from infant development both point to an early role of common motion cues for object grouping. Here we explore the possibility that the privileged status of motion in the developmental timeline is not happenstance, but rather serves to bootstrap the learning of static Gestalt cues. Our approach involves computational analyses of real-world motion sequences to investigate whether primitive optic flow information is correlated with static figural cues that could eventually come to serve as proxies for grouping in the form of Gestalt principles. We calculated local optic flow maps and then examined how similarity of motion across image patches co-varied with similarity of certain figural properties in static frames. Results indicate that patches with similar motion are much more likely to have similar luminance, color, and orientation as compared to patches with dissimilar motion vectors. This regularity suggests that, in principle, common motion extracted from dynamic visual experience can provide enough information to bootstrap region grouping based on luminance and color and contour continuation mechanisms in static scenes. These observations, coupled with the cited experimental studies, lend credence to the hypothesis that static Gestalt laws might be learned through a bootstrapping process based on early dynamic experience.

link (url) DOI [BibTex]

2007

link (url) DOI [BibTex]


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Neuromotor prosthesis development

Donoghue, J., Hochberg, L., Nurmikko, A., Black, M., Simeral, J., Friehs, G.

Medicine & Health Rhode Island, 90(1):12-15, January 2007 (article)

Abstract
Article describes a neuromotor prosthesis (NMP), in development at Brown University, that records human brain signals, decodes them, and transforms them into movement commands. An NMP is described as a system consisting of a neural interface, a decoding system, and a user interface, also called an effector; a closed-loop system would be completed by a feedback signal from the effector to the brain. The interface is based on neural spiking, a source of information-rich, rapid, complex control signals from the nervous system. The NMP described, named BrainGate, consists of a match-head sized platform with 100 thread-thin electrodes implanted just into the surface of the motor cortex where commands to move the hand emanate. Neural signals are decoded by a rack of computers that displays the resultant output as the motion of a cursor on a computer monitor. While computer cursor motion represents a form of virtual device control, this same command signal could be routed to a device to command motion of paralyzed muscles or the actions of prosthetic limbs. The researchers’ overall goal is the development of a fully implantable, wireless multi-neuron sensor for broad research, neural prosthetic, and human neurodiagnostic applications.

pdf [BibTex]

pdf [BibTex]


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On the spatial statistics of optical flow

Roth, S., Black, M. J.

International Journal of Computer Vision, 74(1):33-50, 2007 (article)

Abstract
We present an analysis of the spatial and temporal statistics of "natural" optical flow fields and a novel flow algorithm that exploits their spatial statistics. Training flow fields are constructed using range images of natural scenes and 3D camera motions recovered from hand-held and car-mounted video sequences. A detailed analysis of optical flow statistics in natural scenes is presented and machine learning methods are developed to learn a Markov random field model of optical flow. The prior probability of a flow field is formulated as a Field-of-Experts model that captures the spatial statistics in overlapping patches and is trained using contrastive divergence. This new optical flow prior is compared with previous robust priors and is incorporated into a recent, accurate algorithm for dense optical flow computation. Experiments with natural and synthetic sequences illustrate how the learned optical flow prior quantitatively improves flow accuracy and how it captures the rich spatial structure found in natural scene motion.

pdf preprint pdf from publisher [BibTex]

pdf preprint pdf from publisher [BibTex]


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Assistive technology and robotic control using MI ensemble-based neural interface systems in humans with tetraplegia

Donoghue, J. P., Nurmikko, A., Black, M. J., Hochberg, L.

Journal of Physiology, Special Issue on Brain Computer Interfaces, 579, pages: 603-611, 2007 (article)

Abstract
This review describes the rationale, early stage development, and initial human application of neural interface systems (NISs) for humans with paralysis. NISs are emerging medical devices designed to allowpersonswith paralysis to operate assistive technologies or to reanimatemuscles based upon a command signal that is obtained directly fromthe brain. Such systems require the development of sensors to detect brain signals, decoders to transformneural activity signals into a useful command, and an interface for the user.We review initial pilot trial results of an NIS that is based on an intracortical microelectrode sensor that derives control signals from the motor cortex.We review recent findings showing, first, that neurons engaged by movement intentions persist in motor cortex years after injury or disease to the motor system, and second, that signals derived from motor cortex can be used by persons with paralysis to operate a range of devices. We suggest that, with further development, this form of NIS holds promise as a useful new neurotechnology for those with limited motor function or communication.We also discuss the additional potential for neural sensors to be used in the diagnosis and management of various neurological conditions and as a new way to learn about human brain function.

pdf preprint pdf from publisher DOI [BibTex]

pdf preprint pdf from publisher DOI [BibTex]

2006


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Bayesian population decoding of motor cortical activity using a Kalman filter

Wu, W., Gao, Y., Bienenstock, E., Donoghue, J. P., Black, M. J.

Neural Computation, 18(1):80-118, 2006 (article)

Abstract
Effective neural motor prostheses require a method for decoding neural activity representing desired movement. In particular, the accurate reconstruction of a continuous motion signal is necessary for the control of devices such as computer cursors, robots, or a patient's own paralyzed limbs. For such applications, we developed a real-time system that uses Bayesian inference techniques to estimate hand motion from the firing rates of multiple neurons. In this study, we used recordings that were previously made in the arm area of primary motor cortex in awake behaving monkeys using a chronically implanted multielectrode microarray. Bayesian inference involves computing the posterior probability of the hand motion conditioned on a sequence of observed firing rates; this is formulated in terms of the product of a likelihood and a prior. The likelihood term models the probability of firing rates given a particular hand motion. We found that a linear gaussian model could be used to approximate this likelihood and could be readily learned from a small amount of training data. The prior term defines a probabilistic model of hand kinematics and was also taken to be a linear gaussian model. Decoding was performed using a Kalman filter, which gives an efficient recursive method for Bayesian inference when the likelihood and prior are linear and gaussian. In off-line experiments, the Kalman filter reconstructions of hand trajectory were more accurate than previously reported results. The resulting decoding algorithm provides a principled probabilistic model of motor-cortical coding, decodes hand motion in real time, provides an estimate of uncertainty, and is straightforward to implement. Additionally the formulation unifies and extends previous models of neural coding while providing insights into the motor-cortical code.

pdf preprint pdf from publisher abstract [BibTex]

2006

pdf preprint pdf from publisher abstract [BibTex]

1998


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Summarization of video-taped presentations: Automatic analysis of motion and gesture

Ju, S. X., Black, M. J., Minneman, S., Kimber, D.

IEEE Trans. on Circuits and Systems for Video Technology, 8(5):686-696, September 1998 (article)

Abstract
This paper presents an automatic system for analyzing and annotating video sequences of technical talks. Our method uses a robust motion estimation technique to detect key frames and segment the video sequence into subsequences containing a single overhead slide. The subsequences are stabilized to remove motion that occurs when the speaker adjusts their slides. Any changes remaining between frames in the stabilized sequences may be due to speaker gestures such as pointing or writing, and we use active contours to automatically track these potential gestures. Given the constrained domain, we define a simple set of actions that can be recognized based on the active contour shape and motion. The recognized actions provide an annotation of the sequence that can be used to access a condensed version of the talk from a Web page.

pdf pdf from publisher DOI [BibTex]

1998

pdf pdf from publisher DOI [BibTex]


Thumb xl bildschirmfoto 2012 12 06 um 12.22.18
Robust anisotropic diffusion

Black, M. J., Sapiro, G., Marimont, D., Heeger, D.

IEEE Transactions on Image Processing, 7(3):421-432, March 1998 (article)

Abstract
Relations between anisotropic diffusion and robust statistics are described in this paper. Specifically, we show that anisotropic diffusion can be seen as a robust estimation procedure that estimates a piecewise smooth image from a noisy input image. The edge-stopping; function in the anisotropic diffusion equation is closely related to the error norm and influence function in the robust estimation framework. This connection leads to a new edge-stopping; function based on Tukey's biweight robust estimator that preserves sharper boundaries than previous formulations and improves the automatic stopping of the diffusion. The robust statistical interpretation also provides a means for detecting the boundaries (edges) between the piecewise smooth regions in an image that has been smoothed with anisotropic diffusion. Additionally, we derive a relationship between anisotropic diffusion and regularization with line processes. Adding constraints on the spatial organization of the line processes allows us to develop new anisotropic diffusion equations that result in a qualitative improvement in the continuity of edges

pdf pdf from publisher [BibTex]

pdf pdf from publisher [BibTex]


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PLAYBOT: A visually-guided robot for physically disabled children

Tsotsos, J. K., Verghese, G., Dickinson, S., Jenkin, M., Jepson, A., Milios, E., Nuflo, F., Stevenson, S., Black, M., Metaxas, D., Culhane, S., Ye, Y., Mann, R.

Image & Vision Computing, Special Issue on Vision for the Disabled, 16(4):275-292, 1998 (article)

Abstract
This paper overviews the PLAYBOT project, a long-term, large-scale research program whose goal is to provide a directable robot which may enable physically disabled children to access and manipulate toys. This domain is the first test domain, but there is nothing inherent in the design of PLAYBOT that prohibits its extension to other tasks. The research is guided by several important goals: vision is the primary sensor; vision is task directed; the robot must be able to visually search its environment; object and event recognition are basic capabilities; environments must be natural and dynamic; users and environments are assumed to be unpredictable; task direction and reactivity must be smoothly integrated; and safety is of high importance. The emphasis of the research has been on vision for the robot this is the most challenging research aspect and the major bottleneck to the development of intelligent robots. Since the control framework is behavior-based, the visual capabilities of PLAYBOT are described in terms of visual behaviors. Many of the components of PLAYBOT are briefly described and several examples of implemented sub-systems are shown. The paper concludes with a description of the current overall system implementation, and a complete example of PLAYBOT performing a simple task.

pdf pdf from publisher DOI [BibTex]

pdf pdf from publisher DOI [BibTex]


Thumb xl bildschirmfoto 2012 12 06 um 12.33.38
EigenTracking: Robust matching and tracking of articulated objects using a view-based representation

Black, M. J., Jepson, A.

International Journal of Computer Vision, 26(1):63-84, 1998 (article)

Abstract
This paper describes an approach for tracking rigid and articulated objects using a view-based representation. The approach builds on and extends work on eigenspace representations, robust estimation techniques, and parameterized optical flow estimation. First, we note that the least-squares image reconstruction of standard eigenspace techniques has a number of problems and we reformulate the reconstruction problem as one of robust estimation. Second we define a “subspace constancy assumption” that allows us to exploit techniques for parameterized optical flow estimation to simultaneously solve for the view of an object and the affine transformation between the eigenspace and the image. To account for large affine transformations between the eigenspace and the image we define a multi-scale eigenspace representation and a coarse-to-fine matching strategy. Finally, we use these techniques to track objects over long image sequences in which the objects simultaneously undergo both affine image motions and changes of view. In particular we use this “EigenTracking” technique to track and recognize the gestures of a moving hand.

pdf pdf from publisher video [BibTex]