Shiv Naga Prasad Vitaladevuni

A visual motion detection circuit suggested by Drosophila connectomics

Animal behaviour arises from computations in neuronal circuits, but our understanding of these computations has been frustrated by the lack of detailed synaptic connection maps, or connectomes. For example, despite intensive investigations over half a century, the neuronal implementation of local motion detection in the insect visual system remains elusive. Here we develop a semi-automated pipeline using electron microscopy to reconstruct a connectome, containing 379 neurons and 8,637 chemical synaptic contacts, within the Drosophila optic medulla. By matching reconstructed neurons to examples from light microscopy, we assigned neurons to cell types and assembled a connectome of the repeating module of the medulla. Within this module, we identified cell types constituting a motion detection circuit, and showed that the connections onto individual motion-sensitive neurons in this circuit were consistent with their direction selectivity. Our results identify cellular targets for future functional investigations, and demonstrate that connectomes can provide key insights into neuronal computations.

Semi-automated reconstruction of neural circuits using electron microscopy.

Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience, and the focus of the nascent field of connectomics. Previously used to reconstruct the C. elegans wiring diagram, serial-section transmission electron microscopy (ssTEM) is a proven technique for the task. However, to reconstruct more complex circuits, ssTEM will require the automation of image processing. We review progress in the processing of electron microscopy images and, in particular, a semi-automated reconstruction pipeline deployed at Janelia Farm. Drosophila circuits underlying identified behaviors are being reconstructed in the pipeline with the goal of generating a complete Drosophila connectome.

Multimodal feature fusion for robust event detection in web videos

Combining multiple low-level visual features is a proven and effective strategy for a range of computer vision tasks. However, limited attention has been paid to combining such features with information from other modalities, such as audio and videotext, for large scale analysis of web videos. In our work, we rigorously analyze and combine a large set of low-level features that capture appearance, color, motion, audio and audio-visual co-occurrence patterns in videos. We also evaluate the utility of high-level (i.e., semantic) visual information obtained from detecting scene, object, and action concepts. Further, we exploit multimodal information by analyzing available spoken and videotext content using state-of-the-art automatic speech recognition (ASR) and videotext recognition systems. We combine these diverse features using a two-step strategy employing multiple kernel learning (MKL) and late score level fusion methods. Based on the TRECVID MED 2011 evaluations for detecting 10 events in a large benchmark set of ~45000 videos, our system showed the best performance among the 19 international teams.

Action recognition using ballistic dynamics

We present a Bayesian framework for action recognition through ballistic dynamics. Psycho-kinesiological studies indicate that ballistic movements form the natural units for human movement planning. The framework leads to an efficient and robust algorithm for temporally segmenting videos into atomic movements. Individual movements are annotated with person-centric morphological labels called ballistic verbs. This is tested on a dataset of interactive movements, achieving high recognition rates. The approach is also applied on a gesture recognition task, improving a previously reported recognition rate from 84% to 92%. Consideration of ballistic dynamics enhances the performance of the popular Motion History Image feature. We also illustrate the approachpsilas general utility on real-world videos. Experiments indicate that the method is robust to view, style and appearance variations.

Co-clustering of image segments using convex optimization applied to EM neuronal reconstruction

This paper addresses the problem of jointly clustering two segmentations of closely correlated images. We focus in particular on the application of reconstructing neuronal structures in over-segmented electron microscopy images. We formulate the problem of co-clustering as a quadratic semi-assignment problem and investigate convex relaxations using semidefinite and linear programming. We further introduce a linear programming method with manageable number of constraints and present an approach for learning the cost function. Our method increases computational efficiency by orders of magnitude while maintaining accuracy, automatically finds the optimal number of clusters, and empirically tends to produce binary assignment solutions. We illustrate our approach in simulations and in experiments with real EM data.

Contour-based joint clustering of multiple segmentations

We present an unsupervised, shape-based method for joint clustering of multiple image segmentations. Given two or more closely-related images, such as nearby frames in a video sequence or images of the same scene taken under different lighting conditions, our method generates a joint segmentation of the images. We introduce a novel contour-based representation that allows us to cast the shape-based joint clustering problem as a quadratic semi-assignment problem. Our score function is additive. We use complex-valued affinities to assess the quality of matching the edge elements at the exterior bounding contour of clusters, while ignoring the contributions of elements that fall in the interior of the clusters. We further combine this contour-based score with region information and use a linear programming relaxation to solve for the joint clusters. We evaluate our approach on the occlusion boundary data-set of Stein et al.

Increasing depth resolution of electron microscopy of neural circuits using sparse tomographic reconstruction

Future progress in neuroscience hinges on reconstruction of neuronal circuits to the level of individual synapses. Because of the specifics of neuronal architecture, imaging must be done with very high resolution and throughput. While Electron Microscopy (EM) achieves the required resolution in the transverse directions, its depth resolution is a severe limitation. Computed tomography (CT) may be used in conjunction with electron microscopy to improve the depth resolution, but this severely limits the throughput since several tens or hundreds of EM images need to be acquired. Here, we exploit recent advances in signal processing to obtain high depth resolution EM images computationally. First, we show that the brain tissue can be represented as sparse linear combination of local basis functions that are thin membrane-like structures oriented in various directions. We then develop reconstruction techniques inspired by compressive sensing that can reconstruct the brain tissue from very few (typically 5) tomographic views of each section. This enables tracing of neuronal connections across layers and, hence, high throughput reconstruction of neural circuits to the level of individual synapses.

Combining multiple kernels for efficient image classification

We investigate the problem of combining multiple feature channels for the purpose of efficient image classification. Discriminative kernel based methods, such as SVMs, have been shown to be quite effective for image classification. To use these methods with several feature channels, one needs to combine base kernels computed from them. Multiple kernel learning is an effective method for combining the base kernels. However, the cost of computing the kernel similarities of a test image with each of the support vectors for all feature channels is extremely high. We propose an alternate method, where training data instances are selected, using AdaBoost, for each of the base kernels. A composite decision function, which can be evaluated by computing kernel similarities with respect to only these chosen instances, is learnt. This method significantly reduces the number of kernel computations required during testing. Experimental results on the benchmark UCI datasets, as well as on a challenging painting dataset, are included to demonstrate the effectiveness of our method.

Electron Microscopy Reconstruction of Brain Structure Using Sparse Representations Over Learned Dictionaries

A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral plane and either high-throughput or high depth resolution but not both. Here, we exploit recent advances in unsupervised learning and signal processing to obtain high depth-resolution EM images computationally without sacrificing throughput. First, we show that the brain tissue can be represented as a sparse linear combination of localized basis functions that are learned using high-resolution datasets. We then develop compressive sensing-inspired techniques that can reconstruct the brain tissue from very few (typically five) tomographic views of each section. This enables tracing of neuronal processes and, hence, high throughput reconstruction of neural circuits on the level of individual synapses.

Multi-channel shape-flow kernel descriptors for robust video event detection and retrieval

Despite the success of spatio-temporal visual features, they are hand-designed and aggregate image or flow gradients using a pre-specified, uniform set of orientation bins. Kernel descriptors [1] generalize such orientation histograms by defining match kernels over image patches, and have shown superior performance for visual object and scene recognition. In our work, we make two contributions: first, we extend kernel descriptors to the spatio-temporal domain to model salient flow, gradient and texture patterns in video. Further, we apply our kernel descriptors to extract features from different color channels. Second, we present a fast algorithm for kernel descriptor computation of O(1) complexity for each pixel in each video patch, producing two orders of magnitude speedup over conventional kernel descriptors and other popular motion features. Our evaluation results on TRECVID MED 2011 dataset indicate that the proposed multi-channel shape-flow kernel descriptors outperform several other features including SIFT, SURF, STIP and Color SIFT.