We present a method for segmenting neuron membranes in 2D electron microscopy imagery. This segmentation task has been a bottleneck to reconstruction efforts of the brain's synaptic circuits. One common problem is the misclassification of blurry membrane fragments as cell interior, which leads to merging of two adjacent neuron sections into one via the blurry membrane region. Human annotators can easily avoid such errors by implicitly performing gap completion, taking into account the continuity of membranes.
Drawing inspiration from these human strategies, we formulate the segmentation task as an edge labeling problem on a graph with local topological constraints. We derive an integer linear program (ILP) that enforces membrane continuity, i.e. the absence of gaps. The cost function of the ILP is the pixel-wise deviation of the segmentation from a priori membrane probabilities derived from the data.
Based on membrane probability maps obtained using random forest classifiers and convolutional neural networks, our method improves the neuron boundary segmentation accuracy compared to a variety of standard segmentation approaches. Our method successfully performs gap completion and leads to fewer topological errors. The method could potentially also be incorporated into other image segmentation pipelines with known topological constraints.
Harvard University（哈佛大学）；John A. Paulson School of Engineering and Applied Sciences（约翰·A·保尔森工程与应用科学学院）
We present an interactive approach to train a deep neural network pixel classifier for the segmentation of neuronal structures. An interactive training scheme reduces the extremely tedious manual annotation task that is typically required for deep networks to perform well on image segmentation problems. Our proposed method employs a feedback loop that captures sparse annotations using a graphical user interface, trains a deep neural network based on recent and past annotations, and displays the prediction output to users in almost real-time. Our implementation of the algorithm also allows mult…
University of California, San Diego（加利福尼亚大学圣地亚哥分校）
In this work, we present the depth-adaptive deep neural network using a depth map for semantic segmentation. Typical deep neural networks receive inputs at the predetermined locations regardless of the distance from the camera. This fixed receptive field presents a challenge to generalize the features of objects at various distances in neural networks. Specifically, the predetermined receptive fields are too small at a short distance, and vice versa. To overcome this challenge, we develop a neural network which is able to adapt the receptive field not only for each layer but also for each neur…
Semantic concept hierarchy is still under-explored for semantic segmentation due to the inefficiency and complicated optimization of incorporating structural inference into dense prediction. This lack of modeling semantic correlations also makes prior works must tune highly-specified models for each task due to the label discrepancy across datasets. It severely limits the generalization capability of segmentation models for open set concept vocabulary and annotation utilization. In this paper, we propose a Dynamic-Structured Semantic Propagation Network (DSSPN) that builds a semantic neuron gr…
Harvard University（哈佛大学）；NIT Karnataka（卡纳塔克国家技术学院）；Technical University of Munich（慕尼黑工业大学）；Donostia International Physics Center (DIPC)（多诺斯蒂亚国际物理中心）；University of the Basque Country (UPV/EHU)（巴斯克大学）；Ikerbasque, Basque Foundation for Science（巴斯克科学基金会）
Segmenting 3D cell nuclei from microscopy image volumes is critical for biological and clinical analysis, enabling the study of cellular expression patterns and cell lineages. However, current datasets for neuronal nuclei usually contain volumes smaller than $10^{\text{-}3}\ mm^3$ with fewer than 500 instances per volume, unable to reveal the complexity in large brain regions and restrict the investigation of neuronal structures. In this paper, we have pushed the task forward to the sub-cubic millimeter scale and curated the NucMM dataset with two fully annotated volumes: one $0.1\ mm^3$ elect…
NeuroNet is a deep convolutional neural network mimicking multiple popular and state-of-the-art brain segmentation tools including FSL, SPM, and MALPEM. The network is trained on 5,000 T1-weighted brain MRI scans from the UK Biobank Imaging Study that have been automatically segmented into brain tissue and cortical and sub-cortical structures using the standard neuroimaging pipelines. Training a single model from these complementary and partially overlapping label maps yields a new powerful "all-in-one", multi-output segmentation tool. The processing time for a single subject is reduced by an …
The Johns Hopkins University（约翰斯·霍普金斯大学）；University of California at Los Angeles（加利福尼亚大学洛杉矶分校）
Recent advances in brain clearing and imaging have made it possible to image entire mammalian brains at sub-micron resolution. These images offer the potential to assemble brain-wide atlases of neuron morphology, but manual neuron reconstruction remains a bottleneck. Several automatic reconstruction algorithms exist, but most focus on single neuron images. In this paper, we present a probabilistic reconstruction method, ViterBrain, which combines a hidden Markov state process that encodes neuron geometry with a random field appearance model of neuron fluorescence. Our method utilizes dynamic p…
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…
University of Paris-Saclay（巴黎萨克雷大学）；CEA（法国原子能和替代能源委员会）；CNRS（法国国家科学研究中心）；WITSEE
Recent studies have demonstrated the superiority of deep learning in medical image analysis, especially in cell instance segmentation, a fundamental step for many biological studies. However, the excellent performance of the neural networks requires training on large, unbiased dataset and annotations, which is labor-intensive and expertise-demanding. This paper presents an end-to-end framework to automatically detect and segment NeuN stained neuronal cells on histological images using only point annotations. Unlike traditional nuclei segmentation with point annotation, we propose using point a…
European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence（佛罗伦萨大学欧洲非线性光谱实验室）；Bioretics SrL（Bioretics SrL公司）；National Institute of Optics, National Research Council (INO-CNR)（国家研究委员会国家光学研究所）；Department of Physics（物理系）
Semantic segmentation of neuronal structures in 3D high-resolution fluorescence microscopy imaging of the human brain cortex can take advantage of bidimensional CNNs, which yield good results in neuron localization but lead to inaccurate surface reconstruction. 3D CNNs, on the other hand, would require manually annotated volumetric data on a large scale and hence considerable human effort. Semi-supervised alternative strategies which make use only of sparse annotations suffer from longer training times and achieved models tend to have increased capacity compared to 2D CNNs, needing more ground…
NCIS: Deep Color Gradient Maps Regression and Three-Class Pixel Classification for Enhanced Neuronal Cell Instance Segmentation in Nissl-Stained Histological Images
London South Bank University（伦敦南岸大学）；University of Padova（帕多瓦大学）
FISBe: A real-world benchmark dataset for instance segmentation of long-range thin filamentous structures
Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC)（亥姆霍兹联合会马克斯·德尔布吕克分子医学中心）；Helmholtz Imaging（亥姆霍兹成像中心）；HHMI Janelia Research Campus（HHMI贾尼亚研究校区）；University of Potsdam（波茨坦大学）；German Cancer Research Center (DKFZ)（德国癌症研究中心）
Carnegie Mellon University（卡内基梅隆大学）；Ryerson University（瑞尔森大学）；Facebook AI Research（Facebook人工智能研究院）
We introduce an approach to integrate segmentation information within a convolutional neural network (CNN). This counter-acts the tendency of CNNs to smooth information across regions and increases their spatial precision. To obtain segmentation information, we set up a CNN to provide an embedding space where region co-membership can be estimated based on Euclidean distance. We use these embeddings to compute a local attention mask relative to every neuron position. We incorporate such masks in CNNs and replace the convolution operation with a "segmentation-aware" variant that allows a neuron …
School of Biomedical Engineering & Imaging Sciences, King’s College London（伦敦国王学院生物医学工程与影像科学学院）
We present a novel method to explicitly incorporate topological prior knowledge into deep learning based segmentation, which is, to our knowledge, the first work to do so. Our method uses the concept of persistent homology, a tool from topological data analysis, to capture high-level topological characteristics of segmentation results in a way which is differentiable with respect to the pixelwise probability of being assigned to a given class. The topological prior knowledge consists of the sequence of desired Betti numbers of the segmentation. As a proof-of-concept we demonstrate our approach…
Spiking Neural Networks (SNNs) have recently emerged as the low-power alternative to Artificial Neural Networks (ANNs) because of their sparse, asynchronous, and binary event-driven processing. Due to their energy efficiency, SNNs have a high possibility of being deployed for real-world, resource-constrained systems such as autonomous vehicles and drones. However, owing to their non-differentiable and complex neuronal dynamics, most previous SNN optimization methods have been limited to image recognition. In this paper, we explore the SNN applications beyond classification and present semantic…
Human brain is a layered structure, and performs not only a feedforward process from a lower layer to an upper layer but also a feedback process from an upper layer to a lower layer. The layer is a collection of neurons, and neural network is a mathematical model of the function of neurons. Although neural network imitates the human brain, everyone uses only feedforward process from the lower layer to the upper layer, and feedback process from the upper layer to the lower layer is not used. Therefore, in this paper, we propose Feedback U-Net using Convolutional LSTM which is the segmentation m…
Faculty of Computer Science, Universiti Teknologi, Malaysia（马来西亚理工大学计算机科学学院）；College of Information Technology, UAE University, UAE（阿联酋大学信息技术学院）
Topological alignments and snakes are used in image processing, particularly in locating object boundaries. Both of them have their own advantages and limitations. To improve the overall image boundary detection system, we focused on developing a novel algorithm for image processing. The algorithm we propose to develop will based on the active contour method in conjunction with topological alignments method to enhance the image detection approach. The algorithm presents novel technique to incorporate the advantages of both Topological Alignments and snakes. Where the initial segmentation by To…
A connectivity graph of neurons at the resolution of single synapses provides scientists with a tool for understanding the nervous system in health and disease. Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain have made reconstructions of neurons possible at the nanometer scale. However, automatic segmentation sometimes struggles to segment large neurons correctly, requiring human effort to proofread its output. General proofreading involves inspecting large volumes to correct segmentation errors at the pixel level, a visu…
Deep learning methods have achieved impressive performance for multi-class medical image segmentation. However, they are limited in their ability to encode topological interactions among different classes (e.g., containment and exclusion). These constraints naturally arise in biomedical images and can be crucial in improving segmentation quality. In this paper, we introduce a novel topological interaction module to encode the topological interactions into a deep neural network. The implementation is completely convolution-based and thus can be very efficient. This empowers us to incorporate th…
As one of the successful Transformer-based models in computer vision tasks, SegFormer demonstrates superior performance in semantic segmentation. Nevertheless, the high computational cost greatly challenges the deployment of SegFormer on edge devices. In this paper, we seek to design a lightweight SegFormer for efficient semantic segmentation. Based on the observation that neurons in SegFormer layers exhibit large variances across different images, we propose a dynamic gated linear layer, which prunes the most uninformative set of neurons based on the input instance. To improve the dynamically…
Topology-Preserving Image Segmentation with Spatial-Aware Persistent Feature Matching
Department of Electrical and Computer Engineering, University of California, San Diego（电气与计算机工程系，加州大学圣地亚哥分校）；Department of Ophthalmology, University of California, San Diego（眼科学系，加州大学圣地亚哥分校）
Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state-of-the-art segmentation perfor- mance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on planes orthogonal to 2D image slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a com- bination of a fully convolutional network (FCN) …
Facebook Connectivity Lab（Facebook连接实验室）；University of Illinois, Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Facebook Core Data Science（Facebook核心数据科学）
Learning from weakly-supervised data is one of the main challenges in machine learning and computer vision, especially for tasks such as image semantic segmentation where labeling is extremely expensive and subjective. In this paper, we propose a novel neural network architecture to perform weakly-supervised learning by suppressing irrelevant neuron activations. It localizes objects of interest by learning from image-level categorical labels in an end-to-end manner. We apply this algorithm to a practical challenge of transforming satellite images into a map of settlements and individual buildi…
This work introduces a new proposal-free instance segmentation method that builds on single-instance segmentation masks predicted across the entire image in a sliding window style. In contrast to related approaches, our method concurrently predicts all masks, one for each pixel, and thus resolves any conflict jointly across the entire image. Specifically, predictions from overlapping masks are combined into edge weights of a signed graph that is subsequently partitioned to obtain all final instances concurrently. The result is a parameter-free method that is strongly robust to noise and priori…
Continuous-tone Simple Points: An $\ell_0$-Norm of Cyclic Gradient for Topology-Preserving Data-Driven Image Segmentation
Laboratory of Mathematics and Complex Systems (Ministry of Education), School of Mathematical Sciences, Beijing Normal University（数学与复杂系统实验室（教育部）, 数学科学学院, 北京师范大学）；State Key Laboratory of Remote Sensing Science, Faculty of Geographical Science, Beijing Normal University（遥感科学国家重点实验室, 地理科学学院, 北京师范大学）
The need of sign language is increasing radically especially to hearing impaired community. Only few research groups try to automatically recognize sign language from video, colored gloves and etc. Their approach requires a valid segmentation of the data that is used for training and of the data that is used to be recognized. Recognition of a sign language image sequence is challenging because of the variety of hand shapes and hand motions. Here, this paper proposes to apply a combination of image segmentation with restoration using topological derivatives for achieving high recognition accura…
Applied Brain Research, Inc（应用大脑研究公司）；Army Research Lab（陆军研究实验室）；University of Waterloo（滑铁卢大学）
We seek to investigate the scalability of neuromorphic computing for computer vision, with the objective of replicating non-neuromorphic performance on computer vision tasks while reducing power consumption. We convert the deep Artificial Neural Network (ANN) architecture U-Net to a Spiking Neural Network (SNN) architecture using the Nengo framework. Both rate-based and spike-based models are trained and optimized for benchmarking performance and power, using a modified version of the ISBI 2D EM Segmentation dataset consisting of microscope images of cells. We propose a partitioning method to …
Technical University of Munich（慕尼黑工业大学）；Imperial College London（伦敦帝国理工学院）；University of Zurich（苏黎世大学）
Image segmentation is a largely researched field where neural networks find vast applications in many facets of technology. Some of the most popular approaches to train segmentation networks employ loss functions optimizing pixel-overlap, an objective that is insufficient for many segmentation tasks. In recent years, their limitations fueled a growing interest in topology-aware methods, which aim to recover the correct topology of the segmented structures. However, so far, none of the existing approaches achieve a spatially correct matching between the topological features of ground truth and …
Heidelberg Collaboratory for Image Processing（海德堡图像处理合作实验室）；Heidelberg University（海德堡大学）
We present an end-to-end learned algorithm for seeded segmentation. Our method is based on the Random Walker algorithm, where we predict the edge weights of the underlying graph using a convolutional neural network. This can be interpreted as learning context-dependent diffusivities for a linear diffusion process. Besides calculating the exact gradient for optimizing these diffusivities, we also propose simplifications that sparsely sample the gradient and still yield competitive results. The proposed method achieves the currently best results on a seeded version of the CREMI neuron segmentati…
Besides per-pixel accuracy, topological correctness is also crucial for the segmentation of images with fine-scale structures, e.g., satellite images and biomedical images. In this paper, by leveraging the theory of digital topology, we identify pixels in an image that are critical for topology. By focusing on these critical pixels, we propose a new homotopy warping loss to train deep image segmentation networks for better topological accuracy. To efficiently identify these topologically critical pixels, we propose a new algorithm exploiting the distance transform. The proposed algorithm, as w…
Stony Brook University（石溪大学）；University of California, San Diego（加利福尼亚大学圣迭戈分校）；Oregon State University（俄勒冈州立大学）
In the segmentation of fine-scale structures from natural and biomedical images, per-pixel accuracy is not the only metric of concern. Topological correctness, such as vessel connectivity and membrane closure, is crucial for downstream analysis tasks. In this paper, we propose a new approach to train deep image segmentation networks for better topological accuracy. In particular, leveraging the power of discrete Morse theory (DMT), we identify global structures, including 1D skeletons and 2D patches, which are important for topological accuracy. Trained with a novel loss based on these global …
CEA-CNRS-UMR 9199, MIRCen（法国原子能委员会-法国国家科学研究中心-混合研究单位9199，分子影像研究中心）；Xi’an University of Technology（西安理工大学）；WITSEE（WITSEE公司）
Cell individualization has a vital role in digital pathology image analysis. Deep Learning is considered as an efficient tool for instance segmentation tasks, including cell individualization. However, the precision of the Deep Learning model relies on massive unbiased dataset and manual pixel-level annotations, which is labor intensive. Moreover, most applications of Deep Learning have been developed for processing oncological data. To overcome these challenges, i) we established a pipeline to synthesize pixel-level labels with only point annotations provided; ii) we tested an ensemble Deep L…
We introduce a method for training neural networks to perform image or volume segmentation in which prior knowledge about the topology of the segmented object can be explicitly provided and then incorporated into the training process. By using the differentiable properties of persistent homology, a concept used in topological data analysis, we can specify the desired topology of segmented objects in terms of their Betti numbers and then drive the proposed segmentations to contain the specified topological features. Importantly this process does not require any ground-truth labels, just prior k…
Hebrew University of Jerusalem（耶路撒冷希伯来大学）；Shandong University（山东大学）；Tel Aviv University（特拉维夫大学）
Contextual information provides important cues for disambiguating visually similar pixels in scene segmentation. In this paper, we introduce a neuron-level Selective Context Aggregation (SCA) module for scene segmentation, comprised of a contextual dependency predictor and a context aggregation operator. The dependency predictor is implicitly trained to infer contextual dependencies between different image regions. The context aggregation operator augments local representations with global context, which is aggregated selectively at each neuron according to its on-the-fly predicted dependencie…
Topology-Guaranteed Image Segmentation: Enforcing Connectivity, Genus, and Width Constraints
Laboratory of Mathematics and Complex Systems (Ministry of Education of China)（数学与复杂系统实验室（教育部））；School of Mathematical Sciences, Beijing Normal University（北京师范大学数学系）；NORCE Norwegian Research Centre（挪威国家研究中心）；Beijing Normal University（北京师范大学）
Topology Optimization in Medical Image Segmentation with Fast Euler Characteristic
Department of Computing, Imperial College London（帝国理工学院计算系）；University of Oxford（牛津大学）；Weill Cornell Medicine（韦尔医学院）；Cornell Tech（康奈尔科技）；TUM University Hospital, Technical University of Munich（慕尼黑技术大学医院）；Friedrich-Alexander-Universität Erlangen-Nürnberg（埃尔兰根-纽伦堡弗里德里希-亚历山大大学）；King’s College London（伦敦国王学院）
Topograph: An efficient Graph-Based Framework for Strictly Topology Preserving Image Segmentation
School of Computation, Information and Technology, Technical University of Munich（慕尼黑工业大学计算、信息与技术学院）；Department of Computing, Imperial College London（帝国理工学院计算系）；Munich Center for Machine Learning（慕尼黑机器学习中心）；Munich Data Science Institute, Technical University of Munich（慕尼黑工业大学慕尼黑数据科学研究所）；Weill Cornell Medicine, Cornell University（康奈尔大学威尔医学院）
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 exploring non-occluding and temporally-adjacent object relationships with bi-directional recurrence. (ii) non-local, which allows exploring long-range object relationships in the temporal domain with skip connections. Our proposed network is end-to-end trainable from an input image to a sequence of object masks, and, compared to methods relying on object bo…
University of Notre Dame（圣母大学）；Harvard University（哈佛大学）
In this paper, we consider the problem of automatically segmenting neuronal cells in dual-color confocal microscopy images. This problem is a key task in various quantitative analysis applications in neuroscience, such as tracing cell genesis in Danio rerio (zebrafish) brains. Deep learning, especially using fully convolutional networks (FCN), has profoundly changed segmentation research in biomedical imaging. We face two major challenges in this problem. First, neuronal cells may form dense clusters, making it difficult to correctly identify all individual cells (even to human experts). Conse…
Facebook AI Research（Facebook人工智能研究院）；INRIA（法国国家信息与自动化研究所）；Ecole CentraleSupélec（中央理工-高等电力学院）
In this work we introduce a time- and memory-efficient method for structured prediction that couples neuron decisions across both space at time. We show that we are able to perform exact and efficient inference on a densely connected spatio-temporal graph by capitalizing on recent advances on deep Gaussian Conditional Random Fields (GCRFs). Our method, called VideoGCRF is (a) efficient, (b) has a unique global minimum, and (c) can be trained end-to-end alongside contemporary deep networks for video understanding. We experiment with multiple connectivity patterns in the temporal domain, and pre…
Motivation: 3D neuron segmentation is a key step for the neuron digital reconstruction, which is essential for exploring brain circuits and understanding brain functions. However, the fine line-shaped nerve fibers of neuron could spread in a large region, which brings great computational cost to the neuron segmentation. Meanwhile, the strong noises and disconnected nerve fibers bring great challenges to the task. Results: In this paper, we propose a 3D wavelet and deep learning based 3D neuron segmentation method. The neuronal image is first partitioned into neuronal cubes to simplify the segm…
University of Maryland Baltimore County（马里兰大学巴尔的摩县分校）；University of Miami（迈阿密大学）
Learning High-Resolution representations is essential for semantic segmentation. Convolutional neural network (CNN)architectures with downstream and upstream propagation flow are popular for segmentation in medical diagnosis. However, due to performing spatial downsampling and upsampling in multiple stages, information loss is inexorable. On the contrary, connecting layers densely on high spatial resolution is computationally expensive. In this work, we devise a Loose Dense Connection Strategy to connect neurons in subsequent layers with reduced parameters. On top of that, using a m-way Tree s…
Boosting 3D Neuron Segmentation with 2D Vision Transformer Pre-trained on Natural Images
School of Computer Science, The University of Sydney（悉尼大学计算机科学学院）；Data61, CSIRO（澳大利亚联邦科学与工业研究组织Data61）；SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University（东南大学SEU-ALLEN联合中心脑与智能研究院）
Diffusion Model-Based Data Augmentation for Enhanced Neuron Segmentation
State Key Laboratory of Brain Cognition（脑认知国家重点实验室）；Brain-inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences（脑启发智能技术，自动化研究所，中国科学院）；School of Future Technology, University of Chinese Academy of Sciences（未来技术学院，中国科学院大学）；School of Artificial Intelligence, University of Chinese Academy of Sciences（人工智能学院，中国科学院大学）
