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Most current state-of-the-art connectome reconstruction pipelines have two major steps: initial pixel-based segmentation with affinity prediction and watershed transform, and refined segmentation by merging over-segmented regions. These methods rely only on local context and are typically agnostic to the underlying biology. Since a few merge errors can lead to several incorrectly merged neuronal processes, these algorithms are currently tuned towards over-segmentation producing an overburden of costly proofreading. We propose a third step for connectomics reconstruction pipelines to refine an over-segmentation using both local and global context with an emphasis on adhering to the underlying biology. We first extract a graph from an input segmentation where nodes correspond to segment labels and edges indicate potential split errors in the over-segmentation. In order to increase throughput and allow for large-scale reconstruction, we employ biologically inspired geometric constraints based on neuron morphology to reduce the number of nodes and edges. Next, two neural networks learn these neuronal shapes to further aid the graph construction process. Lastly, we reformulate the region merging problem as a graph partitioning one to leverage global context. We demonstrate the performance of our approach on four real-world connectomics datasets with an average variation of information improvement of 21.3%.

The prospect of neural reconstruction from Electron Microscopy (EM) images has been elucidated by the automatic segmentation algorithms. Although segmentation algorithms eliminate the necessity of tracing the neurons by hand, significant manual effort is still essential for correcting the mistakes they make. A considerable amount of human labor is also required for annotating groundtruth volumes for training the classifiers of a segmentation framework. It is critically important to diminish the dependence on human interaction in the overall reconstruction system. This study proposes a novel classifier training algorithm for EM segmentation aimed to reduce the amount of manual effort demanded by the groundtruth annotation and error refinement tasks. Instead of using an exhaustive pixel level groundtruth, an active learning algorithm is proposed for sparse labeling of pixel and boundaries of superpixels. Because over-segmentation errors are in general more tolerable and easier to correct than the under-segmentation errors, our algorithm is designed to prioritize minimization of false-merges over false-split mistakes. Our experiments on both 2D and 3D data suggest that the proposed method yields segmentation outputs that are more amenable to neural reconstruction than those of existing methods.

Modeling objects using formal grammars has recently regained much attention in computer vision. Probabilistic logic programming, such as Bilattice based Logical Reasoning (BLR), is shown to produce impressive results in object detection/recognition. Although hierarchical object descriptions are preferred in high-level vision tasks for several reasons, BLR has been applied to non-hierarchical object grammars (compositional descriptions of object class). To better align logic programs (esp. BLR) with compositional object hierarchies, we provide a formal grammar, which can guide domain experts to describe objects. That is, we introduce a context-sensitive specification grammar or a meta-grammar, the language of which is the set of all possible object grammars. We show the practicality of the approach by an automatic compiler that translates example object grammars into a BLR logic program and applied it for detecting Graphical User Interface (GUI) components.

This study formulates the IR target detection as a binary classification problem of each pixel. Each pixel is associated with a label which indicates whether it is a target or background pixel. The optimal label set for all the pixels of an image maximizes a posterior distribution of label configuration given the pixel intensities. The posterior probability is factored into (or proportional to) a conditional likelihood of the intensity values and a prior probability of label configuration. Each of these two probabilities are computed assuming a Markov Random Field (MRF) on both pixel intensities and their labels. In particular, this study enforces neighborhood dependency on both intensity values, by a Simultaneous Auto Regressive (SAR) modle, and on labels, by an Auto-Logistic model. The parameters of these MRF models are learned from labeled examples. During testing, an MRF inference technique, namely Iterated Conditional Mode (ICM), produces the optimal label for each pixel. High performances on benchmark datasets demonstrate effectiveness of this method for IR target detection.

The affinity matrix plays the central role in similarity based clustering algorithm. A recent study has shown that, conventional affinity matrices constructed using local neighborhood information are deficient to represent the overall structure of the dataset. In this paper, we propose a novel similarity measure between two points that captures the global setting of the dataset. The proposed affinity measure between two samples is essentially a likelihood that the two samples should fall into the same cluster. To calculate this, we first calculate a pairwise similarity value given a small subset of the data. The distances from a (randomly selected) subset of datapoints to all observations were utilized to produce an intermediate bipartition of the dataset. The outcomes of these bi-partitions provide the subset dependent ‘vote’ in favor of two samples to belong to the same group. These votes are later marginalized to determine the final pairwise similarity values. We achieved better clustering results both synthetic and real images show using affinity matrices learned by proposed voting method than results using the traditional affinity matrices.

Online boosting methods have recently been used successfully for tracking, background subtraction etc. Conventional online boosting algorithms emphasize on interchanging new weak classifiers/features to adapt with the change over time. We are proposing a new online boosting algorithm where the form of the weak classifiers themselves are modified to cope with scene changes. Instead of replacement, the parameters of the weak classifiers are altered in accordance with the new data subset presented to the online boosting process at each time step. Thus we may avoid altogether the issue of how many weak classifiers to be replaced to capture the change in the data or which efficient search algorithm to use for a fast retrieval of weak classifiers. A computationally efficient method has been used in this paper for the adaptation of linear weak classifiers. The proposed algorithm has been implemented to be used both as an online learning and a tracking method. We show quantitative and qualitative results on both UCI datasets and several video sequences to demonstrate improved performance of our algorithm.

Background subtraction is a widely used paradigm to detect moving objects in video taken from a static camera and is used for various important applications such as video surveillance, human motion analysis, etc. Various statistical approaches have been proposed for modeling a given scene background. However, there is no theoretical framework for choosing which features to use to model different regions of the scene background. In this paper we introduce a novel framework for feature selection for background modeling and subtraction. A boosting algorithm, namely RealBoost, is used to choose the best combination of features at each pixel. Given the probability estimates from a pool of features calculated by Kernel Density Estimate (KDE) over a certain time period, the algorithm selects the most useful ones to discriminate foreground objects from the scene background. The results show that the proposed framework successfully selects appropriate features for different parts of the image.