Focused Proofreading: Efficiently Extracting Connectomes from Segmented EM Images

Identifying complex neural circuitry from electron microscopic (EM) images may help unlock the mysteries of the brain. However, identifying this circuitry requires time-consuming, manual tracing (proofreading) due to the size and intricacy of these image datasets, thus limiting state-of-the-art analysis to very small brain regions. Potential avenues to improve scalability include automatic image segmentation and crowd sourcing, but current efforts have had limited success. In this paper, we propose a new strategy, focused proofreading, that works with automatic segmentation and aims to limit proofreading to the regions of a dataset that are most impactful to the resulting circuit. We then introduce a novel workflow, which exploits biological information such as synapses, and apply it to a large dataset in the fly optic lobe. With our techniques, we achieve significant tracing speedups of 3-5x without sacrificing the quality of the resulting circuit. Furthermore, our methodology makes the task of proofreading much more accessible and hence potentially enhances the effectiveness of crowd sourcing

A Bayesian Approach to Manifold Topology Reconstruction

In this paper, we investigate the problem of statistical reconstruction of piecewise linear manifold topology. Given a noisy, probably undersampled point cloud from a one- or two-manifold, the algorithm reconstructs an approximated most likely mesh in a Bayesian sense from which the sample might have been taken. We incorporate statistical priors on the object geometry to improve the reconstruction quality if additional knowledge about the class of original shapes is available. The priors can be formulated analytically or learned from example geometry with known manifold tessellation. The statistical objective function is approximated by a linear programming / integer programming problem, for which a globally optimal solution is found. We apply the algorithm to a set of 2D and 3D reconstruction examples, demon-strating that a statistics-based manifold reconstruction is feasible, and still yields plausible results in situations where sampling conditions are violated

Connectivity-Enforcing Hough Transform for the Robust Extraction of Line Segments

Global voting schemes based on the Hough transform (HT) have been widely used to robustly detect lines in images. However, since the votes do not take line connectivity into account, these methods do not deal well with cluttered images. In opposition, the so-called local methods enforce connectivity but lack robustness to deal with challenging situations that occur in many realistic scenarios, e.g., when line segments cross or when long segments are corrupted. In this paper, we address the critical limitations of the HT as a line segment extractor by incorporating connectivity in the voting process. This is done by only accounting for the contributions of edge points lying in increasingly larger neighborhoods and whose position and directional content agree with potential line segments. As a result, our method, which we call STRAIGHT (Segment exTRAction by connectivity-enforcInG HT), extracts the longest connected segments in each location of the image, thus also integrating into the HT voting process the usually separate step of individual segment extraction. The usage of the Hough space mapping and a corresponding hierarchical implementation make our approach computationally feasible. We present experiments that illustrate, with synthetic and real images, how STRAIGHT succeeds in extracting complete segments in several situations where current methods fail.Comment: Submitted for publicatio

Exploiting line metric reconstruction from non-central circular panoramas

In certain non-central imaging systems, straight lines are projected via a non-planar surface encapsulating the 4 degrees of freedom of the 3D line. Consequently the geometry of the 3D line can be recovered from a minimum of four image points. However, with classical non-central catadioptric systems there is not enough effective baseline for a practical implementation of the method. In this paper we propose a multi-camera system configuration resembling the circular panoramic model which results in a particular non-central projection allowing the stitching of a non-central panorama. From a single panorama we obtain well-conditioned 3D reconstruction of lines, which are specially interesting in texture-less scenarios. No previous information about the direction or arrangement of the lines in the scene is assumed. The proposed method is evaluated on both synthetic and real images

Shape basis interpretation for monocular deformable 3D reconstruction

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.In this paper, we propose a novel interpretable shape model to encode object non-rigidity. We first use the initial frames of a monocular video to recover a rest shape, used later to compute a dissimilarity measure based on a distance matrix measurement. Spectral analysis is then applied to this matrix to obtain a reduced shape basis, that in contrast to existing approaches, can be physically interpreted. In turn, these pre-computed shape bases are used to linearly span the deformation of a wide variety of objects. We introduce the low-rank basis into a sequential approach to recover both camera motion and non-rigid shape from the monocular video, by simply optimizing the weights of the linear combination using bundle adjustment. Since the number of parameters to optimize per frame is relatively small, specially when physical priors are considered, our approach is fast and can potentially run in real time. Validation is done in a wide variety of real-world objects, undergoing both inextensible and extensible deformations. Our approach achieves remarkable robustness to artifacts such as noisy and missing measurements and shows an improved performance to competing methods.Peer ReviewedPostprint (author's final draft

Learning to Construct 3D Building Wireframes from 3D Line Clouds

Line clouds, though under-investigated in the previous work, potentially encode more compact structural information of buildings than point clouds extracted from multi-view images. In this work, we propose the first network to process line clouds for building wireframe abstraction. The network takes a line cloud as input , i.e., a nonstructural and unordered set of 3D line segments extracted from multi-view images, and outputs a 3D wireframe of the underlying building, which consists of a sparse set of 3D junctions connected by line segments. We observe that a line patch, i.e., a group of neighboring line segments, encodes sufficient contour information to predict the existence and even the 3D position of a potential junction, as well as the likelihood of connectivity between two query junctions. We therefore introduce a two-layer Line-Patch Transformer to extract junctions and connectivities from sampled line patches to form a 3D building wireframe model. We also introduce a synthetic dataset of multi-view images with ground-truth 3D wireframe. We extensively justify that our reconstructed 3D wireframe models significantly improve upon multiple baseline building reconstruction methods. The code and data can be found at https://github.com/Luo1Cheng/LC2WF.Comment: 10 pages, 6 figure

Structured Indoor Modeling

In this dissertation, we propose data-driven approaches to reconstruct 3D models for indoor scenes which are represented in a structured way (e.g., a wall is represented by a planar surface and two rooms are connected via the wall). The structured representation of models is more application ready than dense representations (e.g., a point cloud), but poses additional challenges for reconstruction since extracting structures requires high-level understanding about geometries. To address this challenging problem, we explore two common structural regularities of indoor scenes: 1) most indoor structures consist of planar surfaces (planarity), and 2) structural surfaces (e.g., walls and floor) can be represented by a 2D floorplan as a top-down view projection (orthogonality). With breakthroughs in data capturing techniques, we develop automated systems to tackle structured modeling problems, namely piece-wise planar reconstruction and floorplan reconstruction, by learning shape priors (i.e., planarity and orthogonality) from data. With structured representations and production-level quality, the reconstructed models have an immediate impact on many industrial applications