Neuroinformatics最新文献

{"title":"<ArticleTitle xmlns:ns0=\"http://www.w3.org/1998/Math/MathML\">Large Scale in vivo Acquisition, Segmentation and 3D Reconstruction of Cortical Vasculature using <ns0:math><ns0:mi>μ</ns0:mi></ns0:math> Doppler Ultrasound Imaging.","authors":"Anoek Strumane, Théo Lambert, Jan Aelterman, Danilo Babin, Gabriel Montaldo, Wilfried Philips, Clément Brunner, Alan Urban","doi":"10.1007/s12021-024-09706-1","DOIUrl":"10.1007/s12021-024-09706-1","url":null,"abstract":"<p><p>The brain is composed of a dense and ramified vascular network of arteries, veins and capillaries of various sizes. One way to assess the risk of cerebrovascular pathologies is to use computational models to predict the physiological effects of reduced blood supply and correlate these responses with observations of brain damage. Therefore, it is crucial to establish a detailed 3D organization of the brain vasculature, which could be used to develop more accurate in silico models. To this end, we have adapted our functional ultrasound imaging platform, previously designed for recording large scale activity, to enable rapid and reproducible acquisition, segmentation and reconstruction of the cortical vasculature. For the first time, it allows us to digitize the cortical <math><mrow><mo>∼</mo> <mn>100</mn></mrow> </math> - <math><mi>μ</mi></math> m3 spatial resolution. Unlike most available strategies, our approach can be performed in vivo within minutes. Moreover, it is easy to implement since it requires neither exogenous contrast agents nor long post-processing time. Therefore, we performed a cortex-wide reconstruction of the vasculature and its quantitative analysis, including i) classification of descending arteries versus ascending veins in more than 1500 vessels/animal and ii) rapid estimation of their length. Importantly, we confirmed the relevance of our approach in a model of cortical stroke, which allows rapid visualization of the ischemic lesion. This development contributes to extending the capabilities of ultrasound neuroimaging to better understand cerebrovascular pathologies such as stroke, vascular cognitive impairment and brain tumors, and is highly scalable for the clinic.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"5"},"PeriodicalIF":2.7,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Classification Prediction of Hydrocephalus After Intercerebral Haemorrhage Based on Machine Learning Approach.","authors":"Enwen Zhu, Zhuojun Zou, Jianxian Li, Jipan Chen, Ao Chen, Naifei Zhao, Qiang Yuan, Caicai Liu, Xin Tang","doi":"10.1007/s12021-024-09710-5","DOIUrl":"https://doi.org/10.1007/s12021-024-09710-5","url":null,"abstract":"<p><p>In order to construct a clinical classification prediction model for hydrocephalus after intercerebral haemorrhage(ICH) to guide clinical treatment decisions, this paper retrospectively analyses the clinical data of 844 cases of ICH and hydrocephalus inpatients admitted to Yueyang People's Hospital from May 2019 to October 2022, of which 95 cases of hydrocephalus occurred after ICH and no hydrocephalus in 749 cases. The following indicators were compared between the two groups of patients: gender, age, Glasgow Coma Scale(GCS)score, whether the amount of bleeding was greater than 30 ml, whether it broke into the ventricle or not, modified Graeb score(MGS), modified Rankin Scale (MRS) score, whether surgery was performed or not, red blood cells, white blood cells, and platelets. After variable screening, the following six variables were selected: GCS score, MGS, MRS score, whether the bleeding volume was greater than 30 ml, whether it broke into the ventricle or not, and whether surgery was performed or not were modelled and analysed using logistic regression model and support vector machine model in machine learning. The results showed that under the same conditions, the accuracy of the support vector machine model was 0.89 and F1 was 0.838 ,the value of the AUC of the support vector machine model is 0.888; the accuracy of the logistic regression model was 0.902 and F1 was 0.89, the value of the AUC of the support vector machine model is 0.903. Compared with the group without hydrocephalus, patients in the group with hydrocephalus had bleeding volume greater than 30 ml, haemorrhage into the ventricles of the brain, and had undergone surgery in the brain, and the difference was statistically significant (P 0.001). Statistical analysis showed that GCS score ≤ 8.8, modified Graeb score (MGS) ≥ 10 and MRS score ≥ 3 were independent risk factors for the development of hydrocephalus after spontaneous ventricular haemorrhage. Therefore, patients with lower GCS score, higher modified Graeb score, higher MRS score, bleeding volume > 30 ml, haemorrhage into the ventricles of the brain, and experience of having undergone surgery in the brain should be operated on early to remove the intraventricular haematoma in order to reduce the incidence of hydrocephalus.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"6"},"PeriodicalIF":2.7,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"\"The Brain is…\": A Survey of the Brain's Many Definitions.","authors":"Taylor Bolt, Lucina Q Uddin","doi":"10.1007/s12021-024-09699-x","DOIUrl":"10.1007/s12021-024-09699-x","url":null,"abstract":"<p><p>A reader of the peer-reviewed neuroscience literature will often encounter expressions like the following: 'the brain is a dynamic system', 'the brain is a complex network', or 'the brain is a highly metabolic organ'. These expressions attempt to define the essential functions and properties of the mammalian or human brain in a simple phrase or sentence, sometimes using metaphors or analogies. We sought to survey the most common phrases of the form 'the brain is…' in the biomedical literature to provide insights into current conceptualizations of the brain. Utilizing text analytic tools applied to a large sample (> 4 million) of peer-reviewed full-text articles and abstracts, we extracted several thousand phrases of the form 'the brain is…' and identified over a dozen frequently appearing phrases. The most used phrases included metaphors (e.g., the brain as a 'information processor' or 'prediction machine') and descriptions of essential functions (e.g., 'a central organ of stress adaptation') or properties (e.g., 'a highly vascularized organ'). Comparison of these phrases with those involving other bodily organs (e.g. the heart, liver, etc.) highlighted common phrases between the brain and other organs, such as the heart as a 'complex, dynamic system'. However, the brain was unique among organs in the number and diversity of analogies ascribed to it. The results of our analysis underscore the diversity of qualities and functions attributed to the brain in the biomedical literature and suggest a range of conceptualizations that defy unification.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"4"},"PeriodicalIF":2.7,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11724787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational Generation of Long-range Axonal Morphologies.","authors":"Adrien Berchet, Remy Petkantchin, Henry Markram, Lida Kanari","doi":"10.1007/s12021-024-09696-0","DOIUrl":"10.1007/s12021-024-09696-0","url":null,"abstract":"<p><p>Long-range axons are fundamental to brain connectivity and functional organization, enabling communication between different brain regions. Recent advances in experimental techniques have yielded a substantial number of whole-brain axonal reconstructions. While previous computational generative models of neurons have predominantly focused on dendrites, generating realistic axonal morphologies is more challenging due to their distinct targeting. In this study, we present a novel algorithm for axon synthesis that combines algebraic topology with the Steiner tree algorithm, an extension of the minimum spanning tree, to generate both the local and long-range compartments of axons. We demonstrate that our computationally generated axons closely replicate experimental data in terms of their morphological properties. This approach enables the generation of biologically accurate long-range axons that span large distances and connect multiple brain regions, advancing the digital reconstruction of the brain. Ultimately, our approach opens up new possibilities for large-scale in-silico simulations, advancing research into brain function and disorders.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"3"},"PeriodicalIF":2.7,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11723904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Automated Lesion and Feature Extraction Pipeline for Brain MRIs with Interpretability.","authors":"Reza Eghbali, Pierre Nedelec, David Weiss, Radhika Bhalerao, Long Xie, Jeffrey D Rudie, Chunlei Liu, Leo P Sugrue, Andreas M Rauschecker","doi":"10.1007/s12021-024-09708-z","DOIUrl":"10.1007/s12021-024-09708-z","url":null,"abstract":"<p><p>This paper introduces the Automated Lesion and Feature Extraction (ALFE) pipeline, an open-source, Python-based pipeline that consumes MR images of the brain and produces anatomical segmentations, lesion segmentations, and human-interpretable imaging features describing the lesions in the brain. ALFE pipeline is modeled after the neuroradiology workflow and generates features that can be used by physicians for quantitative analysis of clinical brain MRIs and for machine learning applications. The pipeline uses a decoupled design which allows the user to customize the image processing, image registrations, and AI segmentation tools without the need to change the business logic of the pipeline. In this manuscript, we give an overview of ALFE, present the main aspects of ALFE pipeline design philosophy, and present case studies.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"2"},"PeriodicalIF":2.7,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11717894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stimulation Effects Mapping for Optimizing Coil Placement for Transcranial Magnetic Stimulation.","authors":"Gangliang Zhong, Fang Jin, Liang Ma, Yongfeng Yang, Baogui Zhang, Dan Cao, Jin Li, Nianming Zuo, Lingzhong Fan, Zhengyi Yang, Tianzi Jiang","doi":"10.1007/s12021-024-09714-1","DOIUrl":"https://doi.org/10.1007/s12021-024-09714-1","url":null,"abstract":"<p><p>The position and orientation of transcranial magnetic stimulation (TMS) coil, which we collectively refer to as coil placement, significantly affect both the assessment and modulation of cortical excitability. TMS electric field (E-field) simulation can be used to identify optimal coil placement. However, the present E-field simulation required a laborious segmentation and meshing procedure to determine optimal coil placement. We intended to create a framework that would enable us to offer optimal coil placement without requiring the segmentation and meshing procedure. We constructed the stimulation effects map (SEM) framework using the CASIA dataset for optimal coil placement. We used leave-one-subject-out cross-validation to evaluate the consistency of the optimal coil placement and the target regions determined by SEM for the 74 target ROIs in MRI data from the CASIA, HCP15 and HCP100 datasets. Additionally, we contrasted the E-norms determined by optimal coil placements using SEM and auxiliary dipole method (ADM) based on the DP and CASIA II datasets. We provided optimal coil placement in 'head-anatomy-based' (HAC) polar coordinates and MNI coordinates for the target region. The results also demonstrated the consistency of the SEM framework for the 74 target ROIs. The normal E-field determined by SEM was more significant than the value received by ADM. We created the SEM framework using the CASIA database to determine optimal coil placement without segmentation or meshing. We provided optimal coil placement in HAC and MNI coordinates for the target region. The validation of several target ROIs from various datasets demonstrated the consistency of the SEM approach. By streamlining the process of finding optimal coil placement, we intended to make TMS assessment and therapy more convenient.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"1"},"PeriodicalIF":2.7,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NeuroCarto: A Toolkit for Building Custom Read-out Channel Maps for High Electrode-count Neural Probes.","authors":"Ta-Shun Su, Fabian Kloosterman","doi":"10.1007/s12021-024-09705-2","DOIUrl":"10.1007/s12021-024-09705-2","url":null,"abstract":"<p><p>Neuropixels probes contain thousands of electrodes across one or more shanks and are sufficiently small to allow chronic recording of neural activity in freely behaving small animals. However, the joint increase in the number of electrodes and miniaturization of the probe package has led to a compromise in which groups of electrodes share a single read-out channel and only a fraction of the electrodes can be read out at any given time. Experimenters then face the challenge of selecting a subset of electrodes (i.e., channel map) that both covers the brain regions of interest and adheres to the restrictions of the underlying hardware. Here, we present NeuroCarto, a Python toolkit and GUI to simplify the construction of a custom channel map for Neuropixels probes. We describe a general iterative approach to select electrodes and provide a specific implementation that allows experimenters to specify a blueprint of regions of interest along the probe shanks and the desired local electrode density. NeuroCarto assists in generating a channel map from the blueprint and visualizes potential read-out channel conflicts. We showcase the utility of NeuroCarto in an experimental workflow to simultaneously record from the dorsal and ventral hippocampus with 4-shank Neuropixels 2.0 probes in freely moving mice.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"16"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Self-supervised Deep Learning Model for Diagonal Sulcus Detection with Limited Labeled Data.","authors":"Delfina Braggio, Hernán C Külsgaard, Mariana Vallejo-Azar, Mariana Bendersky, Paula González, Lucía Alba-Ferrara, José Ignacio Orlando, Ignacio Larrabide","doi":"10.1007/s12021-024-09700-7","DOIUrl":"10.1007/s12021-024-09700-7","url":null,"abstract":"<p><p>Sulci are a fundamental part of brain morphology, closely linked to brain function, cognition, and behavior. Tertiary sulci, characterized as the shallowest and smallest subtype, pose a challenging task for detection. The diagonal sulcus (ds), located in a crucial area in language processing, has a prevalence between 50% and 60%. Automatic detection of the ds is an unexplored field: while some sulci segmenters include the ds, their accuracy is usually low. In this work, we present a deep learning based model for ds detection using a fine-tuning approach with limited training labeled data. A convolutional autoencoder was employed to learn specific features related to brain morphology with unlabeled data through self-supervised learning. Subsequently, the pre-trained network was fine-tuned to detect the ds using a less extensive labeled dataset. We achieved a mean F1-score of 0.7176 (SD=0.0736) for the test set and a F1-score of 0.72 for a second held-out set, surpassing the results of a standard software and other alternative deep learning models. We conducted an interpretability analysis of the results using occlusion maps and observed that the models focused on adjacent sulci to the ds for prediction, consistent with the approach taken by experts in manual annotation. We also analyzed the challenges of manual labeling by conducting a thorough examination of interrater agreement on a small dataset and its relationship with our model's performance. Finally, we applied our method on a population analysis and reported the prevalence of ds in a case study.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"13"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance of Convolutional Neural Network Models in Meningioma Segmentation in Magnetic Resonance Imaging: A Systematic Review and Meta-Analysis.","authors":"Ting-Wei Wang, Jia-Sheng Hong, Wei-Kai Lee, Yi-Hui Lin, Huai-Che Yang, Cheng-Chia Lee, Hung-Chieh Chen, Hsiu-Mei Wu, Weir Chiang You, Yu-Te Wu","doi":"10.1007/s12021-024-09704-3","DOIUrl":"10.1007/s12021-024-09704-3","url":null,"abstract":"<p><strong>Background: </strong>Meningioma, the most common primary brain tumor, presents significant challenges in MRI-based diagnosis and treatment planning due to its diverse manifestations. Convolutional Neural Networks (CNNs) have shown promise in improving the accuracy and efficiency of meningioma segmentation from MRI scans. This systematic review and meta-analysis assess the effectiveness of CNN models in segmenting meningioma using MRI.</p><p><strong>Methods: </strong>Following the PRISMA guidelines, we searched PubMed, Embase, and Web of Science from their inception to December 20, 2023, to identify studies that used CNN models for meningioma segmentation in MRI. Methodological quality of the included studies was assessed using the CLAIM and QUADAS-2 tools. The primary variable was segmentation accuracy, which was evaluated using the Sørensen-Dice coefficient. Meta-analysis, subgroup analysis, and meta-regression were performed to investigate the effects of MRI sequence, CNN architecture, and training dataset size on model performance.</p><p><strong>Results: </strong>Nine studies, comprising 4,828 patients, were included in the analysis. The pooled Dice score across all studies was 89% (95% CI: 87-90%). Internal validation studies yielded a pooled Dice score of 88% (95% CI: 85-91%), while external validation studies reported a pooled Dice score of 89% (95% CI: 88-90%). Models trained on multiple MRI sequences consistently outperformed those trained on single sequences. Meta-regression indicated that training dataset size did not significantly influence segmentation accuracy.</p><p><strong>Conclusion: </strong>CNN models are highly effective for meningioma segmentation in MRI, particularly during the use of diverse datasets from multiple MRI sequences. This finding highlights the importance of data quality and imaging sequence selection in the development of CNN models. Standardization of MRI data acquisition and preprocessing may improve the performance of CNN models, thereby facilitating their clinical adoption for the optimal diagnosis and treatment of meningioma.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"14"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation Study of Envelope Wave Electrical Nerve Stimulation Based on a Real Head Model.","authors":"Yuhao Liu, Renling Zou, Liang Zhao, Linpeng Jin, Xiufang Hu, Xuezhi Yin","doi":"10.1007/s12021-024-09711-4","DOIUrl":"10.1007/s12021-024-09711-4","url":null,"abstract":"<p><p>In recent years, the modulation of brain neural activity by applied electromagnetic fields has become a hot spot in neuroscience research. Transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS) are two common non-invasive neuromodulation techniques. However, conventional tACS has limited stimulation effects in the deeper parts of the brain. In this study, a method of low and medium frequency envelope wave neurostimulation is proposed, and its effectiveness and safety are evaluated by simulation and human experiment. First, we built a real head model from head MRI image data and used the finite element method to calculate the current distribution of the envelope wave in the brain. Then, a single-compartment neuron model was constructed in NEURON software to simulate the action potential generation of neurons under different frequencies of electrical stimulation. Finally, a human experiment was conducted to investigate the threshold of human perception of envelope wave electrical stimulation. The results show that envelope wave can both increase the depth of stimulation and induce neurons to generate effective action potentials. In envelope wave electrical stimulation, the optimal modulating wave frequency was 50 Hz, and the carrier frequency was 2 kHz-3 kHz. This method is expected to play an important role in the non-invasive treatment of neurological and psychiatric disorders.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":"23 1","pages":"15"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}