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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…

Neural circuits can be reconstructed from brain images acquired by serial section electron microscopy. Image analysis has been performed by manual labor for half a century, and efforts at automation date back almost as far. Convolutional…

Convolutional neural networks are state-of-the-art for various segmentation tasks. While for 2D images these networks are also computationally efficient, 3D convolutions have huge storage requirements and therefore, end-to-end training is…

We present a recurrent network for the 3D reconstruction of neurons that sequentially generates binary masks for every object in an image with spatio-temporal consistency. Our network models consistency in two parts: (i) local, which allows…

Feedforward multilayer networks trained by supervised learning have recently demonstrated state of the art performance on image labeling problems such as boundary prediction and scene parsing. As even very low error rates can limit…

Automatic 3D neuron reconstruction is critical for analysing the morphology and functionality of neurons in brain circuit activities. However, the performance of existing tracing algorithms is hinged by the low image quality. Recently, a…

For the past decade, convolutional networks have been used for 3D reconstruction of neurons from electron microscopic (EM) brain images. Recent years have seen great improvements in accuracy, as evidenced by submissions to the SNEMI3D…

The current neuron reconstruction pipeline for electron microscopy (EM) data usually includes automatic image segmentation followed by extensive human expert proofreading. In this work, we aim to reduce human workload by predicting…

Digital neuron reconstruction from 3D microscopy images is an essential technique for investigating brain connectomics and neuron morphology. Existing reconstruction frameworks use convolution-based segmentation networks to partition the…

We show dense voxel embeddings learned via deep metric learning can be employed to produce a highly accurate segmentation of neurons from 3D electron microscopy images. A "metric graph" on a set of edges between voxels is constructed from…

Convolutional Neural Networks (CNN) have been regarded as a powerful class of models for image recognition problems. Nevertheless, it is not trivial when utilizing a CNN for learning spatio-temporal video representation. A few studies have…

Neuron reconstruction, one of the fundamental tasks in neuroscience, rebuilds neuronal morphology from 3D light microscope imaging data. It plays a critical role in analyzing the structure-function relationship of neurons in the nervous…

Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm…

State-of-the-art image segmentation algorithms generally consist of at least two successive and distinct computations: a boundary detection process that uses local image information to classify image locations as boundaries between objects,…

Deep learning approaches to 3D shape segmentation are typically formulated as a multi-class labeling problem. Existing models are trained for a fixed set of labels, which greatly limits their flexibility and adaptivity. We opt for top-down…

Convolutional Neural Networks (CNNs) have achieved promising results in medical image segmentation. However, CNNs require lots of training data and are incapable of handling pose and deformation of objects. Furthermore, their pooling layers…

Deep-neural-network-based image reconstruction has demonstrated promising performance in medical imaging for under-sampled and low-dose scenarios. However, it requires large amount of memory and extensive time for the training. It is…

The field of connectomics has recently produced neuron wiring diagrams from relatively large brain regions from multiple animals. Most of these neural reconstructions were computed from isotropic (e.g., FIBSEM) or near isotropic (e.g.,…

In this paper we address the memory demands that come with the processing of 3-dimensional, high-resolution, multi-channeled medical images in deep learning. We exploit memory-efficient backpropagation techniques, to reduce the memory…

To build the connectomics map of the brain, we developed a new algorithm that can automatically refine the Membrane Detection Probability Maps (MDPM) generated to perform automatic segmentation of electron microscopy (EM) images. To achieve…