The brain is the least explored organ in the human body. Brain functions are realized through a complex neural network composed of a vast number of neurons, and understanding the morphology of these neurons is base to brain studies. However, obtaining high-quality, large-scale data on neuron morphology remains a significant challenge. In this study, we propose a precise data-graded allocation method for neuron reconstruction, the accuracy is safeguarded by the allocation algorithm and the quantitative model. Reconstruction efficiency was improved by optimizing automated reconstruction algorithm, human-machine interaction workflow and human-task matching method. We have implemented this strategy on a web-based platform, and the results show that 92.9% of image data can be easily reconstructed, thereby reducing the skill requirements for participant. The reconstruction accuracy is 98.2%$\pm$3.1%, better than existing methods. We also provides meticulously annotated datasets that can propel significant advancements in artificial intelligence technology. In addition, we can offer a well-balance across quality, cost, and efficiency, sharing a more flexible and versatile solution for three-dimensional neuron reconstruction.

MOTIVATION: Neuroscientists have long endeavored to map brain connectivity, yet the intricate nature of brain networks often leads them to concentrate on specific regions, hindering efforts to unveil a comprehensive connectivity map. Recent advancements in imaging and text mining techniques have enabled the accumulation of a vast body of literature containing valuable insights into brain connectivity, facilitating the extraction of whole-brain connectivity relations from this corpus. However, the diverse representations of brain region names and connectivity relations pose a challenge for conventional machine learning methods and dictionary-based approaches in identifying all instances accurately. RESULTS: We propose BioSEPBERT, a biomedical pre-trained model based on start-end position pointers and BERT. In addition, our model integrates specialized identifiers with enhanced self-attention capabilities for preceding and succeeding brain regions, thereby improving the performance of named entity recognition and relation extraction in neuroscience. Our approach achieves optimal F1 scores of 85.0%, 86.6%, and 86.5% for named entity recognition, connectivity relation extraction, and directional relation extraction, respectively, surpassing state-of-the-art models by 2.6%, 1.1%, and 1.1%. Furthermore, we leverage BioSEPBERT to extract 22.6 million standardized brain regions and 165 072 directional relations from a corpus comprising 1.3 million abstracts and 193 100 full-text articles. The results demonstrate that our model facilitates researchers to rapidly acquire knowledge regarding neural circuits across various brain regions, thereby enhancing comprehension of brain connectivity in specific regions. AVAILABILITY AND IMPLEMENTATION: Data and source code are available at: http://atlas.brainsmatics.org/res/BioSEPBERT and https://github.com/Brainsmatics/BioSEPBERT.

Clarifying the morphological characteristics of neurons can promote the understanding of brain function. However, traditional morphometrics fail to capture the modeling of each point in reconstructed neurons, leading to limited ability to distinguish massive nerve fibers and restricted application scenarios. To address these challenges, we propose MorphoGNN, a single neuron morphological embedding based on a graph neural network in this study. MorphoGNN learns the point-level structure information of reconstructed nerve fibers by considering their nearest neighbors on each hidden layer. This enables MorphoGNN to capture the lower-dimensional representation of a single neuron through an end-to-end model. In order to meet the requirements of various tasks, both supervised and self-supervised training strategies are designed to learn the characteristics that fit artificial semantics or the morphological patterns of neurons, respectively. We quantitatively compare our embeddings with other features in neuron classification and retrieval tasks and demonstrate cutting-edge performance. Additionally, we introduce our embeddings to the task of reconstruction quality classification and neuron clustering, where they can help detect reconstruction errors and obtain similar subtyping results to existing work. Furthermore, our method can be handily combined with other modal features, such as microscopic image features and traditional morphometrics. Ablation and robustness tests are also conducted to analyze the impact of several network components and low-quality reconstructed neurons on the performance of our method. The code is available at https://github.com/fun0515/MorphoGNN.

BACKGROUND: Neurons are the basic structural unit of the brain, and their morphology is a key determinant of their classification. The morphology of a neuronal circuit is a fundamental component in neuron modeling. Recently, single-neuron morphologies of the whole brain have been used in many studies. The correctness and completeness of semimanually traced neuronal morphology are credible. However, there are some inaccuracies in semimanual tracing results. The distance between consecutive nodes marked by humans is very long, spanning multiple voxels. On the other hand, the nodes are marked around the centerline of the neuronal fiber, not on the centerline. Although these inaccuracies do not seriously affect the projection patterns that these studies focus on, they reduce the accuracy of the traced neuronal skeletons. These small inaccuracies will introduce deviations into subsequent studies that are based on neuronal morphology files. RESULTS: We propose a neuronal digital skeleton optimization method to evaluate and make fine adjustments to a digital skeleton after neuron tracing. Provided that the neuronal fiber shape is smooth and continuous, we describe its physical properties according to two shape restrictions. One restriction is designed based on the grayscale image, and the other is designed based on geometry. These two restrictions are designed to finely adjust the digital skeleton points to the neuronal fiber centerline. With this method, we design the three-dimensional shape restriction workflow of neuronal skeleton adjustment computation. The performance of the proposed method has been quantitatively evaluated using synthetic and real neuronal image data. The results show that our method can reduce the difference between the traced neuronal skeleton and the centerline of the neuronal fiber. Furthermore, morphology metrics such as the neuronal fiber length and radius become more precise. CONCLUSIONS: This method can improve the accuracy of a neuronal digital skeleton based on traced results. The greater the accuracy of the digital skeletons that are acquired, the more precise the neuronal morphologies that are analyzed will be.

This paper studies a class of heterogeneous delayed impulsive neural networks with memristors and their collective evolution for multisynchronization. The multisynchronization represents a diversified collective behavior that is inspired by multitasking as well as observations of heterogeneity and hybridity arising from system models. In view of memristor, the memristor-based impulsive neural network is first represented by an impulsive differential inclusion. According to the memristive and impulsive mechanism, a fuzzy logic rule is introduced, and then, a new fuzzy hybrid impulsive and switching control method is presented correspondingly. It is shown that using the proposed fuzzy hybrid control scheme, multisynchronization of interconnected memristor-based impulsive neural networks can be guaranteed with a positive exponential convergence rate. The heterogeneity and hybridity in system models, thus, can be indicated by the obtained error thresholds that contribute to the multisynchronization. Numerical examples are presented and compared to demonstrate the effectiveness of the developed theoretical results.

The performance of photoacoustic microscopy (PAM) degrades due to the turbidity of the skull that introduces attenuation and distortion of both laser and stimulated ultrasound. In this manuscript, we demonstrated that a newly developed skull optical clearing solution (SOCS) could enhance not only the transmittance of light, but also that of ultrasound in the skull in vitro. Thus the photoacoustic signal was effectively elevated, and the relative strength of the artifacts induced by the skull could be suppressed. Furthermore in vivo studies demonstrated that SOCS could drastically enhance the performance of photoacoustic microscopy for cerebral microvasculature imaging.

The connection study between biological structure and function, as well as between anatomical data and mechanical or physiological models, has been of increasing significance with the rapid advancement in experimental physiology and computational physiology. The China Physiome Project (CPP) is dedicated in optimization of the connection exploration based on standardization and integration of the structural datasets and their derivatives of cryosectional images with various standards, collaboration mechanisms, and online services. The CPP framework hereby incorporates the three-dimensional anatomical models of human and rat anatomy, the finite-element models of whole-body human skeleton, and the multiparticle radiological dosimetry data of both the human and rat computational phantoms. The ontology of CPP was defined using MeSH and, with its all standardized models description implemented by M3L, a multiscale modeling language based on XML. Provided services based on Wiki concept include collaboration research, modeling version control, data sharing, online analysis of M3L documents. As a sample case, a multiscale model for human heart modeling, in which familiar hypertrophic cardiomyopathy was studied according to the structure-function relations from genetic level to organ level, is integrated into the framework and given for demonstration of the functionality of multiscale physiological modeling based on CPP.

BACKGROUND: The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the Resource Description Framework (RDF) data file provided by the GO consortium: 1) Lack of sufficient semantic relationships between pairs of terms coming from the three independent GO sub-ontologies, that limit the power to provide complex semantic queries and inference services based on it. 2) The term-centric view of GO annotation data and the fact that all information is stored in a single file. This makes attempts to retrieve GO annotations based on big volume datasets unmanageable. 3) No support of GOSlim. RESULTS: We propose a RDF model, GORouter, which encodes heterogeneous original data in a uniform RDF format, creates additional ontology mappings between GO terms, and introduces a set of inference rulebases. Furthermore, we use the Oracle Network Data Model (NDM) as the native RDF data repository and the table function RDF_MATCH to seamlessly combine the result of RDF queries with traditional relational data. As a result, the scale of GORouter is minimized; information not directly involved in semantic inference is put into relational tables. CONCLUSION: Our work demonstrates how to use multiple semantic web tools and techniques to provide a mixture of semantic query and inference solutions of GO and its associations. GORouter is licensed under Apache License Version 2.0, and is accessible via the website: http://www.scbit.org/gorouter/.