737 research outputs found

    On morphological hierarchical representations for image processing and spatial data clustering

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    Hierarchical data representations in the context of classi cation and data clustering were put forward during the fties. Recently, hierarchical image representations have gained renewed interest for segmentation purposes. In this paper, we briefly survey fundamental results on hierarchical clustering and then detail recent paradigms developed for the hierarchical representation of images in the framework of mathematical morphology: constrained connectivity and ultrametric watersheds. Constrained connectivity can be viewed as a way to constrain an initial hierarchy in such a way that a set of desired constraints are satis ed. The framework of ultrametric watersheds provides a generic scheme for computing any hierarchical connected clustering, in particular when such a hierarchy is constrained. The suitability of this framework for solving practical problems is illustrated with applications in remote sensing

    Recursive Training of 2D-3D Convolutional Networks for Neuronal Boundary Detection

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    Efforts to automate the reconstruction of neural circuits from 3D electron microscopic (EM) brain images are critical for the field of connectomics. An important computation for reconstruction is the detection of neuronal boundaries. Images acquired by serial section EM, a leading 3D EM technique, are highly anisotropic, with inferior quality along the third dimension. For such images, the 2D max-pooling convolutional network has set the standard for performance at boundary detection. Here we achieve a substantial gain in accuracy through three innovations. Following the trend towards deeper networks for object recognition, we use a much deeper network than previously employed for boundary detection. Second, we incorporate 3D as well as 2D filters, to enable computations that use 3D context. Finally, we adopt a recursively trained architecture in which a first network generates a preliminary boundary map that is provided as input along with the original image to a second network that generates a final boundary map. Backpropagation training is accelerated by ZNN, a new implementation of 3D convolutional networks that uses multicore CPU parallelism for speed. Our hybrid 2D-3D architecture could be more generally applicable to other types of anisotropic 3D images, including video, and our recursive framework for any image labeling problem

    Multi-stage Multi-recursive-input Fully Convolutional Networks for Neuronal Boundary Detection

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    In the field of connectomics, neuroscientists seek to identify cortical connectivity comprehensively. Neuronal boundary detection from the Electron Microscopy (EM) images is often done to assist the automatic reconstruction of neuronal circuit. But the segmentation of EM images is a challenging problem, as it requires the detector to be able to detect both filament-like thin and blob-like thick membrane, while suppressing the ambiguous intracellular structure. In this paper, we propose multi-stage multi-recursive-input fully convolutional networks to address this problem. The multiple recursive inputs for one stage, i.e., the multiple side outputs with different receptive field sizes learned from the lower stage, provide multi-scale contextual boundary information for the consecutive learning. This design is biologically-plausible, as it likes a human visual system to compare different possible segmentation solutions to address the ambiguous boundary issue. Our multi-stage networks are trained end-to-end. It achieves promising results on two public available EM segmentation datasets, the mouse piriform cortex dataset and the ISBI 2012 EM dataset.Comment: Accepted by ICCV201

    Large Scale Image Segmentation with Structured Loss based Deep Learning for Connectome Reconstruction

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    We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a 3D U-NET, trained to predict affinities between voxels, followed by iterative region agglomeration. We train using a structured loss based on MALIS, encouraging topologically correct segmentations obtained from affinity thresholding. Our extension consists of two parts: First, we present a quasi-linear method to compute the loss gradient, improving over the original quadratic algorithm. Second, we compute the gradient in two separate passes to avoid spurious gradient contributions in early training stages. Our predictions are accurate enough that simple learning-free percentile-based agglomeration outperforms more involved methods used earlier on inferior predictions. We present results on three diverse EM datasets, achieving relative improvements over previous results of 27%, 15%, and 250%. Our findings suggest that a single method can be applied to both nearly isotropic block-face EM data and anisotropic serial sectioned EM data. The runtime of our method scales linearly with the size of the volume and achieves a throughput of about 2.6 seconds per megavoxel, qualifying our method for the processing of very large datasets

    Image Segmentation from RGBD Images by 3D Point Cloud Attributes and High-Level Features

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    In this paper, an approach is developed for segmenting an image into major surfaces and potential objects using RGBD images and 3D point cloud data retrieved from a Kinect sensor. In the proposed segmentation algorithm, depth and RGB data are mapped together. Color, texture, XYZ world coordinates, and normal-, surface-, and graph-based segmentation index features are then generated for each pixel point. These attributes are used to cluster similar points together and segment the image. The inclusion of new depth-related features provided improved segmentation performance over RGB-only algorithms by resolving illumination and occlusion problems that cannot be handled using graph-based segmentation algorithms, as well as accurately identifying pixels associated with the main structure components of rooms (walls, ceilings, floors). Since each segment is a potential object or structure, the output of this algorithm is intended to be used for object recognition. The algorithm has been tested on commercial building images and results show the usability of the algorithm in real time applications
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