Related papers: Robust neural circuit reconstruction from serial e…

Electron microscopic connectomics is an ambitious research direction with the goal of studying comprehensive brain connectivity maps by using high-throughput, nano-scale microscopy. One of the main challenges in connectomics research is…

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…

Deep learning has been shown to produce state of the art results in many tasks in biomedical imaging, especially in segmentation. Moreover, segmentation of the cerebrovascular structure from magnetic resonance angiography is a challenging…

We propose a new STAckable Recurrent cell (STAR) for recurrent neural networks (RNNs), which has fewer parameters than widely used LSTM and GRU while being more robust against vanishing or exploding gradients. Stacking recurrent units into…

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…

Developing automated and semi-automated solutions for reconstructing wiring diagrams of the brain from electron micrographs is important for advancing the field of connectomics. While the ultimate goal is to generate a graph of neuron…

Segmentation has been a major task in neuroimaging. A large number of automated methods have been developed for segmenting healthy and diseased brain tissues. In recent years, deep learning techniques have attracted a lot of attention as a…

In the field of Connectomics, a primary problem is that of 3D neuron segmentation. Although deep learning-based methods have achieved remarkable accuracy, errors still exist, especially in regions with image defects. One common type of…

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…

This tutorial covers biomedical image reconstruction, from the foundational concepts of system modeling and direct reconstruction to modern sparsity and learning-based approaches. Imaging is a critical tool in biological research and…

In recent years, significant progress has been made in the medical image analysis domain using convolutional neural networks (CNNs). In particular, deep neural networks based on a U-shaped architecture (UNet) with skip connections have been…

Connectomics is an emerging field in neuroscience that aims to reconstruct the 3-dimensional morphology of neurons from electron microscopy (EM) images. Recent studies have successfully demonstrated the use of convolutional neural networks…

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…

The advent of comprehensive synaptic wiring diagrams of large neural circuits has created the field of connectomics and given rise to a number of open research questions. One such question is whether it is possible to reconstruct the…

The emerging field of connectomics aims to unlock the mysteries of the brain by understanding the connectivity between neurons. To map this connectivity, we acquire thousands of electron microscopy (EM) images with nanometer-scale…

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…

Semantic image segmentation is one of the most important tasks in medical image analysis. Most state-of-the-art deep learning methods require a large number of accurately annotated examples for model training. However, accurate annotation…

Reconstructing the intricate local morphology of neurons and their long-range projecting axons can address many connectivity related questions in neuroscience. The main bottleneck in connectomics pipelines is correcting topological errors,…

The field of connectomics faces unprecedented "big data" challenges. To reconstruct neuronal connectivity, automated pixel-level segmentation is required for petabytes of streaming electron microscopy data. Existing algorithms provide…

Magnetic resonance imaging (MRI) is a valuable clinical tool for displaying anatomical structures and aiding in accurate diagnosis. Medical image super-resolution (SR) reconstruction using deep learning techniques can enhance lesion…