An Out-of-Domain Synapse Detection Challenge for Microwasp Brain Connectomes
Flatiron Institute（熨斗研究所）；Harvard University（哈佛大学）；Birla Institute of Technology and Science-Pilani（比尔拉科学技术学院-皮拉尼）；Lomonosov Moscow State University（莫斯科国立罗蒙诺索夫大学）；Boston College（波士顿学院）
Jingpeng Wu, Yicong Li, Nishika Gupta, Kazunori Shinomiya, Pat Gunn, Alexey Polilov, Hanspeter Pfister, Dmitri Chklovskii, Donglai Wei
The size of image stacks in connectomics studies now reaches the terabyte and often petabyte scales with a great diversity of appearance across brain regions and samples. However, manual annotation of neural structures, e.g., synapses, is time-consuming, which leads to limited training data often smaller than 0.001\% of the test data in size. Domain adaptation and generalization approaches were proposed to address similar issues for natural images, which were less evaluated on connectomics data due to a lack of out-of-domain benchmarks.
Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience and becoming a focus of the emerging field of connectomics. To date, electron microscopy (EM) is the most proven technique for identifying and quantifying synaptic connections. As advances in EM make acquiring larger datasets possible, subsequent manual synapse identification ({\em i.e.}, proofreading) for deciphering a connectome becomes a major time bottleneck. Here we introduce a large-scale, high-throughput, and semi-automated methodology to efficiently identify synapses. We successfully applied …
Functional connectivity (FC) between regions of the brain can be assessed by the degree of temporal correlation measured with functional neuroimaging modalities. Based on the fact that these connectivities build a network, graph-based approaches for analyzing the brain connectome have provided insights into the functions of the human brain. The development of graph neural networks (GNNs) capable of learning representation from graph structured data has led to increased interest in learning the graph representation of the brain connectome. Although recent attempts to apply GNN to the FC network…
Universiti Teknologi Malaysia（马来西亚理工大学）；King Abdullah University of Science and Technology（阿卜杜拉国王科技大学）
We exploit altered patterns in brain functional connectivity as features for automatic discriminative analysis of neuropsychiatric patients. Deep learning methods have been introduced to functional network classification only very recently for fMRI, and the proposed architectures essentially focused on a single type of connectivity measure. We propose a deep convolutional neural network (CNN) framework for classification of electroencephalogram (EEG)-derived brain connectome in schizophrenia (SZ). To capture complementary aspects of disrupted connectivity in SZ, we explore combination of vario…
Harvard University（哈佛大学）；Max Planck Institute for Brain Research（马克斯·普朗克大脑研究所）
Synaptic connectivity detection is a critical task for neural reconstruction from Electron Microscopy (EM) data. Most of the existing algorithms for synapse detection do not identify the cleft location and direction of connectivity simultaneously. The few methods that computes direction along with contact location have only been demonstrated to work on either dyadic (most common in vertebrate brain) or polyadic (found in fruit fly brain) synapses, but not on both types. In this paper, we present an algorithm to automatically predict the location as well as the direction of both dyadic and poly…
Harbin Institute of Technology at Shenzhen（哈尔滨工业大学（深圳））；Peng Cheng Laboratory（鹏城实验室）
Multi-modal neuroimaging technology has greatlly facilitated the efficiency and diagnosis accuracy, which provides complementary information in discovering objective disease biomarkers. Conventional deep learning methods, e.g. convolutional neural networks, overlook relationships between nodes and fail to capture topological properties in graphs. Graph neural networks have been proven to be of great importance in modeling brain connectome networks and relating disease-specific patterns. However, most existing graph methods explicitly require known graph structures, which are not available in t…
ConnectomeBench2: A Unified Benchmark for Automated Connectomic Proofreading
MIT（麻省理工学院）；The Open University（开放大学）；Mindspan Institute（Mindspan研究所）；Yang Tan Collective（杨谭集团）；McGovern Institute（麦戈文研究所）；MIT Departments of Brain and Cognitive Sciences and Biological Engineering（麻省理工学院脑与认知科学系和生物工程系）
Extracting a connectome from an electron microscopy (EM) data set requires identification of neurons and determination of synapses between neurons. As manual extraction of this information is very time-consuming, there has been extensive research effort to automatically segment the neurons to help guide and eventually replace manual tracing. Until recently, there has been comparatively less research on automatically detecting the actual synapses between neurons. This discrepancy can, in part, be attributed to several factors: obtaining neuronal shapes is a prerequisite first step in extracting…
Duke University（杜克大学）；Allen Institute for Brain Sciences（艾伦脑科学研究所）；Johns Hopkins University（约翰斯·霍普金斯大学）；Stanford University School of Medicine（斯坦福大学医学院）；University of North Carolina（北卡罗来纳大学）
Brain function results from communication between neurons connected by complex synaptic networks. Synapses are themselves highly complex and diverse signaling machines, containing protein products of hundreds of different genes, some in hundreds of copies, arranged in precise lattice at each individual synapse. Synapses are fundamental not only to synaptic network function but also to network development, adaptation, and memory. In addition, abnormalities of synapse numbers or molecular components are implicated in most mental and neurological disorders. Despite their obvious importance, mamma…
Recent neuroimaging studies have shown that functional connectomes are unique to individuals, i.e., two distinct fMRIs taken over different sessions of the same subject are more similar in terms of their connectomes than those from two different subjects. In this study, we present significant new results that identify, for the first time, specific parts of resting-state and task-specific connectomes that code the unique signatures. We show that a very small part of the connectome codes the signatures. A network of these features is shown to achieve excellent training and test accuracy in match…
University of Utah（犹他大学）；Florida State University（佛罗里达州立大学）；University of Vienna（维也纳大学）；University of Virginia（弗吉尼亚大学）
The goal of diffusion-weighted magnetic resonance imaging (DWI) is to infer the structural connectivity of an individual subject's brain in vivo. To statistically study the variability and differences between normal and abnormal brain connectomes, a mathematical model of the neural connections is required. In this paper, we represent the brain connectome as a Riemannian manifold, which allows us to model neural connections as geodesics. This leads to the challenging problem of estimating a Riemannian metric that is compatible with the DWI data, i.e., a metric such that the geodesic curves repr…
Kharkevich Institute for Information Transmission Problems（哈尔克维奇信息传输问题研究所）；University of Southern California（南加州大学）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究所）
In this work, we study the extent to which structural connectomes and topological derivative measures are unique to individual changes within human brains. To do so, we classify structural connectome pairs from two large longitudinal datasets as either belonging to the same individual or not. Our data is comprised of 227 individuals from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and 226 from the Parkinson's Progression Markers Initiative (PPMI). We achieve 0.99 area under the ROC curve score for features which represent either weights or network structure of the connectomes (node …
Istanbul Technical University（伊斯坦布尔理工大学）；BASIRA Lab（巴希拉实验室）
Catchy but rigorous deep learning architectures were tailored for image super-resolution (SR), however, these fail to generalize to non-Euclidean data such as brain connectomes. Specifically, building generative models for super-resolving a low-resolution (LR) brain connectome at a higher resolution (HR) (i.e., adding new graph nodes/edges) remains unexplored although this would circumvent the need for costly data collection and manual labelling of anatomical brain regions (i.e. parcellation). To fill this gap, we introduce GSR-Net (Graph Super-Resolution Network), the first super-resolution f…
Bridging Brain Connectomes and Clinical Reports for Early Alzheimer's Disease Diagnosis
The University of Texas at Arlington（德克萨斯大学阿灵顿分校）；Indiana University Indianapolis（印第安纳大学印第安纳波利斯分校）；University of Cambridge（剑桥大学）；University of Sheffield（谢菲尔德大学）；The University of Georgia（佐治亚大学）
Lehigh University（利哈伊大学）；Cumberland Valley High School（坎伯兰谷高中）；Beihang University（北京航空航天大学）；Emory University（埃默里大学）；University of Illinois at Chicago（伊利诺伊大学芝加哥分校）
This paper presents a novel graph-based kernel learning approach for connectome analysis. Specifically, we demonstrate how to leverage the naturally available structure within the graph representation to encode prior knowledge in the kernel. We first proposed a matrix factorization to directly extract structural features from natural symmetric graph representations of connectome data. We then used them to derive a structure-persevering graph kernel to be fed into the support vector machine. The proposed approach has the advantage of being clinically interpretable. Quantitative evaluations on c…
Vision Research Lab, University of California, Santa Barbara（加州大学圣巴巴拉分校视觉研究实验室）；UC Irvine Health, University of California, Irvine（加州大学尔湾分校医疗中心）
This paper introduces a novel methodology to integrate human brain connectomics and parcellation for brain tumor segmentation and survival prediction. For segmentation, we utilize an existing brain parcellation atlas in the MNI152 1mm space and map this parcellation to each individual subject data. We use deep neural network architectures together with hard negative mining to achieve the final voxel level classification. For survival prediction, we present a new method for combining features from connectomics data, brain parcellation information, and the brain tumor mask. We leverage the avera…
Kharkevich Institute for Information Transmission Problems（哈尔克维奇信息传输问题研究所）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术学院）；National Research University Higher School of Economics（国家研究型高等经济大学）
In this paper, we tackle a problem of predicting phenotypes from structural connectomes. We propose that normalized Laplacian spectra can capture structural properties of brain networks, and hence graph spectral distributions are useful for a task of connectome-based classification. We introduce a kernel that is based on earth mover's distance (EMD) between spectral distributions of brain networks. We access performance of an SVM classifier with the proposed kernel for a task of classification of autism spectrum disorder versus typical development based on a publicly available dataset. Classif…
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 p…
