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Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration.
Current approaches for dynamic profiling of single cells rely on dissociated cultures, which lack important biological features existing in tissues. Organotypic slice cultures preserve aspects of structural and synaptic organisation within the brain and are amenable to microscopy, but established techniques are not well adapted for high throughput or longitudinal single cell analysis. Here we developed a custom-built, automated confocal imaging platform, with improved organotypic slice culture and maintenance. The approach enables fully automated image acquisition and four-dimensional tracking of morphological changes within individual cells in organotypic cultures from rodent and human primary tissues for at least 3 weeks. To validate this system, we analysed neurons expressing a disease-associated version of huntingtin (HTT586Q138-EGFP), and observed that they displayed hallmarks of Huntington's disease and died sooner than controls. By facilitating longitudinal single-cell analyses of neuronal physiology, our system bridges scales necessary to attain statistical power to detect developmental and disease phenotypes
Vision-Based Production of Personalized Video
In this paper we present a novel vision-based system for the automated production of personalised video souvenirs for visitors in leisure and cultural heritage venues. Visitors are visually identified and tracked through a camera network. The system produces a personalized DVD souvenir at the end of a visitor’s stay allowing visitors to relive their experiences. We analyze how we identify visitors by fusing facial and body features, how we track visitors, how the tracker recovers from failures due to occlusions, as well as how we annotate and compile the final product. Our experiments demonstrate the feasibility of the proposed approach
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Array atomic force microscopy for real-time multiparametric analysis.
Nanoscale multipoint structure-function analysis is essential for deciphering the complexity of multiscale biological and physical systems. Atomic force microscopy (AFM) allows nanoscale structure-function imaging in various operating environments and can be integrated seamlessly with disparate probe-based sensing and manipulation technologies. Conventional AFMs only permit sequential single-point analysis; widespread adoption of array AFMs for simultaneous multipoint study is challenging owing to the intrinsic limitations of existing technological approaches. Here, we describe a prototype dispersive optics-based array AFM capable of simultaneously monitoring multiple probe-sample interactions. A single supercontinuum laser beam is utilized to spatially and spectrally map multiple cantilevers, to isolate and record beam deflection from individual cantilevers using distinct wavelength selection. This design provides a remarkably simplified yet effective solution to overcome the optical cross-talk while maintaining subnanometer sensitivity and compatibility with probe-based sensors. We demonstrate the versatility and robustness of our system on parallel multiparametric imaging at multiscale levels ranging from surface morphology to hydrophobicity and electric potential mapping in both air and liquid, mechanical wave propagation in polymeric films, and the dynamics of living cells. This multiparametric, multiscale approach provides opportunities for studying the emergent properties of atomic-scale mechanical and physicochemical interactions in a wide range of physical and biological networks
Articulated human tracking and behavioural analysis in video sequences
Recently, there has been a dramatic growth of interest in the observation and tracking
of human subjects through video sequences. Arguably, the principal impetus has come
from the perceived demand for technological surveillance, however applications in entertainment,
intelligent domiciles and medicine are also increasing. This thesis examines
human articulated tracking and the classi cation of human movement, rst separately
and then as a sequential process.
First, this thesis considers the development and training of a 3D model of human body
structure and dynamics. To process video sequences, an observation model is also designed
with a multi-component likelihood based on edge, silhouette and colour. This is de ned on
the articulated limbs, and visible from a single or multiple cameras, each of which may be
calibrated from that sequence. Second, for behavioural analysis, we develop a methodology
in which actions and activities are described by semantic labels generated from a Movement
Cluster Model (MCM). Third, a Hierarchical Partitioned Particle Filter (HPPF) was
developed for human tracking that allows multi-level parameter search consistent with the
body structure. This tracker relies on the articulated motion prediction provided by the
MCM at pose or limb level. Fourth, tracking and movement analysis are integrated to
generate a probabilistic activity description with action labels.
The implemented algorithms for tracking and behavioural analysis are tested extensively
and independently against ground truth on human tracking and surveillance
datasets. Dynamic models are shown to predict and generate synthetic motion, while
MCM recovers both periodic and non-periodic activities, de ned either on the whole body
or at the limb level. Tracking results are comparable with the state of the art, however
the integrated behaviour analysis adds to the value of the approach.Overseas Research Students Awards Scheme (ORSAS
Spatiotemporal visual analysis of human actions
In this dissertation we propose four methods for the recognition of human activities. In all four of
them, the representation of the activities is based on spatiotemporal features that are automatically
detected at areas where there is a significant amount of independent motion, that is, motion that is
due to ongoing activities in the scene. We propose the use of spatiotemporal salient points as features
throughout this dissertation. The algorithms presented, however, can be used with any kind of features,
as long as the latter are well localized and have a well-defined area of support in space and time. We
introduce the utilized spatiotemporal salient points in the first method presented in this dissertation.
By extending previous work on spatial saliency, we measure the variations in the information content of
pixel neighborhoods both in space and time, and detect the points at the locations and scales for which
this information content is locally maximized. In this way, an activity is represented as a collection of
spatiotemporal salient points. We propose an iterative linear space-time warping technique in order
to align the representations in space and time and propose to use Relevance Vector Machines (RVM)
in order to classify each example into an action category. In the second method proposed in this
dissertation we propose to enhance the acquired representations of the first method. More specifically,
we propose to track each detected point in time, and create representations based on sets of trajectories,
where each trajectory expresses how the information engulfed by each salient point evolves over time.
In order to deal with imperfect localization of the detected points, we augment the observation model
of the tracker with background information, acquired using a fully automatic background estimation
algorithm. In this way, the tracker favors solutions that contain a large number of foreground pixels.
In addition, we perform experiments where the tracked templates are localized on specific parts of the
body, like the hands and the head, and we further augment the tracker’s observation model using a
human skin color model. Finally, we use a variant of the Longest Common Subsequence algorithm
(LCSS) in order to acquire a similarity measure between the resulting trajectory representations, and
RVMs for classification. In the third method that we propose, we assume that neighboring salient
points follow a similar motion. This is in contrast to the previous method, where each salient point was
tracked independently of its neighbors. More specifically, we propose to extract a novel set of visual
descriptors that are based on geometrical properties of three-dimensional piece-wise polynomials. The
latter are fitted on the spatiotemporal locations of salient points that fall within local spatiotemporal
neighborhoods, and are assumed to follow a similar motion. The extracted descriptors are invariant in
translation and scaling in space-time. Coupling the neighborhood dimensions to the scale at which the
corresponding spatiotemporal salient points are detected ensures the latter. The descriptors that are
extracted across the whole dataset are subsequently clustered in order to create a codebook, which is
used in order to represent the overall motion of the subjects within small temporal windows.Finally,we use boosting in order to select the most discriminative of these windows for each class, and RVMs for
classification. The fourth and last method addresses the joint problem of localization and recognition
of human activities depicted in unsegmented image sequences. Its main contribution is the use of an
implicit representation of the spatiotemporal shape of the activity, which relies on the spatiotemporal
localization of characteristic ensembles of spatiotemporal features. The latter are localized around
automatically detected salient points. Evidence for the spatiotemporal localization of the activity
is accumulated in a probabilistic spatiotemporal voting scheme. During training, we use boosting in
order to create codebooks of characteristic feature ensembles for each class. Subsequently, we construct
class-specific spatiotemporal models, which encode where in space and time each codeword ensemble
appears in the training set. During testing, each activated codeword ensemble casts probabilistic
votes concerning the spatiotemporal localization of the activity, according to the information stored
during training. We use a Mean Shift Mode estimation algorithm in order to extract the most probable
hypotheses from each resulting voting space. Each hypothesis corresponds to a spatiotemporal volume
which potentially engulfs the activity, and is verified by performing action category classification with
an RVM classifier
SALSA: A Novel Dataset for Multimodal Group Behavior Analysis
Studying free-standing conversational groups (FCGs) in unstructured social
settings (e.g., cocktail party ) is gratifying due to the wealth of information
available at the group (mining social networks) and individual (recognizing
native behavioral and personality traits) levels. However, analyzing social
scenes involving FCGs is also highly challenging due to the difficulty in
extracting behavioral cues such as target locations, their speaking activity
and head/body pose due to crowdedness and presence of extreme occlusions. To
this end, we propose SALSA, a novel dataset facilitating multimodal and
Synergetic sociAL Scene Analysis, and make two main contributions to research
on automated social interaction analysis: (1) SALSA records social interactions
among 18 participants in a natural, indoor environment for over 60 minutes,
under the poster presentation and cocktail party contexts presenting
difficulties in the form of low-resolution images, lighting variations,
numerous occlusions, reverberations and interfering sound sources; (2) To
alleviate these problems we facilitate multimodal analysis by recording the
social interplay using four static surveillance cameras and sociometric badges
worn by each participant, comprising the microphone, accelerometer, bluetooth
and infrared sensors. In addition to raw data, we also provide annotations
concerning individuals' personality as well as their position, head, body
orientation and F-formation information over the entire event duration. Through
extensive experiments with state-of-the-art approaches, we show (a) the
limitations of current methods and (b) how the recorded multiple cues
synergetically aid automatic analysis of social interactions. SALSA is
available at http://tev.fbk.eu/salsa.Comment: 14 pages, 11 figure
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