Neuroinformatics最新文献

{"title":"Towards Automated Brain Aneurysm Detection in TOF-MRA: Open Data, Weak Labels, and Anatomical Knowledge.","authors":"Tommaso Di Noto,&nbsp;Guillaume Marie,&nbsp;Sebastien Tourbier,&nbsp;Yasser Alemán-Gómez,&nbsp;Oscar Esteban,&nbsp;Guillaume Saliou,&nbsp;Meritxell Bach Cuadra,&nbsp;Patric Hagmann,&nbsp;Jonas Richiardi","doi":"10.1007/s12021-022-09597-0","DOIUrl":"https://doi.org/10.1007/s12021-022-09597-0","url":null,"abstract":"<p><p>Brain aneurysm detection in Time-Of-Flight Magnetic Resonance Angiography (TOF-MRA) has undergone drastic improvements with the advent of Deep Learning (DL). However, performances of supervised DL models heavily rely on the quantity of labeled samples, which are extremely costly to obtain. Here, we present a DL model for aneurysm detection that overcomes the issue with \"weak\" labels: oversized annotations which are considerably faster to create. Our weak labels resulted to be four times faster to generate than their voxel-wise counterparts. In addition, our model leverages prior anatomical knowledge by focusing only on plausible locations for aneurysm occurrence. We first train and evaluate our model through cross-validation on an in-house TOF-MRA dataset comprising 284 subjects (170 females / 127 healthy controls / 157 patients with 198 aneurysms). On this dataset, our best model achieved a sensitivity of 83%, with False Positive (FP) rate of 0.8 per patient. To assess model generalizability, we then participated in a challenge for aneurysm detection with TOF-MRA data (93 patients, 20 controls, 125 aneurysms). On the public challenge, sensitivity was 68% (FP rate = 2.5), ranking 4th/18 on the open leaderboard. We found no significant difference in sensitivity between aneurysm risk-of-rupture groups (p = 0.75), locations (p = 0.72), or sizes (p = 0.15). Data, code and model weights are released under permissive licenses. We demonstrate that weak labels and anatomical knowledge can alleviate the necessity for prohibitively expensive voxel-wise annotations.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9931814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9323605","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":"ABLE: Automated Brain Lines Extraction Based on Laplacian Surface Collapse.","authors":"Alberto Fernández-Pena,&nbsp;Daniel Martín de Blas,&nbsp;Francisco J Navas-Sánchez,&nbsp;Luis Marcos-Vidal,&nbsp;Pedro M Gordaliza,&nbsp;Javier Santonja,&nbsp;Joost Janssen,&nbsp;Susanna Carmona,&nbsp;Manuel Desco,&nbsp;Yasser Alemán-Gómez","doi":"10.1007/s12021-022-09601-7","DOIUrl":"https://doi.org/10.1007/s12021-022-09601-7","url":null,"abstract":"<p><p>The archetypical folded shape of the human cortex has been a long-standing topic for neuroscientific research. Nevertheless, the accurate neuroanatomical segmentation of sulci remains a challenge. Part of the problem is the uncertainty of where a sulcus transitions into a gyrus and vice versa. This problem can be avoided by focusing on sulcal fundi and gyral crowns, which represent the topological opposites of cortical folding. We present Automated Brain Lines Extraction (ABLE), a method based on Laplacian surface collapse to reliably segment sulcal fundi and gyral crown lines. ABLE is built to work on standard FreeSurfer outputs and eludes the delineation of anastomotic sulci while maintaining sulcal fundi lines that traverse the regions with the highest depth and curvature. First, it segments the cortex into gyral and sulcal surfaces; then, each surface is spatially filtered. A Laplacian-collapse-based algorithm is applied to obtain a thinned representation of the surfaces. This surface is then used for careful detection of the endpoints of the lines. Finally, sulcal fundi and gyral crown lines are obtained by eroding the surfaces while preserving the connectivity between the endpoints. The method is validated by comparing ABLE with three other sulcal extraction methods using the Human Connectome Project (HCP) test-retest database to assess the reproducibility of the different tools. The results confirm ABLE as a reliable method for obtaining sulcal lines with an accurate representation of the sulcal topology while ignoring anastomotic branches and the overestimation of the sulcal fundi lines. ABLE is publicly available via https://github.com/HGGM-LIM/ABLE .</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9338839","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":"Assessing the Repeatability of Multi-Frequency Multi-Layer Brain Network Topologies Across Alternative Researcher's Choice Paths.","authors":"Stavros I Dimitriadis","doi":"10.1007/s12021-022-09610-6","DOIUrl":"10.1007/s12021-022-09610-6","url":null,"abstract":"<p><p>There is a growing interest in the neuroscience community on the advantages of multilayer functional brain networks. Researchers usually treated different frequencies separately at distinct functional brain networks. However, there is strong evidence that these networks share complementary information while their interdependencies could reveal novel findings. For this purpose, neuroscientists adopt multilayer networks, which can be described mathematically as an extension of trivial single-layer networks. Multilayer networks have become popular in neuroscience due to their advantage to integrate different sources of information. Here, Ι will focus on the multi-frequency multilayer functional connectivity analysis on resting-state fMRI (rs-fMRI) recordings. However, constructing a multilayer network depends on selecting multiple pre-processing steps that can affect the final network topology. Here, I analyzed the rs-fMRI dataset from a single human performing scanning over a period of 18 months (84 scans in total), and the rs-fMRI dataset containing 25 subjects with 3 repeat scans. I focused on assessing the reproducibility of multi-frequency multilayer topologies exploring the effect of two filtering methods for extracting frequencies from BOLD activity, three connectivity estimators, with or without a topological filtering scheme, and two spatial scales. Finally, I untangled specific combinations of researchers' choices that yield consistently brain networks with repeatable topologies, giving me the chance to recommend best practices over consistent topologies.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10776639","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":"Semi-Automated Quantitative Evaluation of Neuron Developmental Morphology In Vitro Using the Change-Point Test.","authors":"Ashlee S Liao,&nbsp;Wenxin Cui,&nbsp;Yongjie Jessica Zhang,&nbsp;Victoria A Webster-Wood","doi":"10.1007/s12021-022-09600-8","DOIUrl":"https://doi.org/10.1007/s12021-022-09600-8","url":null,"abstract":"<p><p>Neuron morphology gives rise to distinct axons and dendrites and plays an essential role in neuronal functionality and circuit dynamics. In rat hippocampal neurons, morphological development occurs over roughly one week in vitro. This development has been qualitatively described as occurring in 5 stages. Still, there is a need to quantify cell growth to monitor cell culture health, understand cell responses to sensory cues, and compare experimental results and computational growth model predictions. To address this need, embryonic rat hippocampal neurons were observed in vitro over six days, and their processes were quantified using both standard morphometrics (degree, number of neurites, total length, and tortuosity) and new metrics (distance between change points, relative turning angle, and the number of change points) based on the Change-Point Test to track changes in path trajectories. Of the standard morphometrics, the total length of neurites per cell and the number of endpoints were significantly different between 0.5, 1.5, and 4 days in vitro, which are typically associated with Stages 2-4. Using the Change-Point Test, the number of change points and the average distance between change points per cell were also significantly different between those key time points. This work highlights key quantitative characteristics, both among common and novel morphometrics, that can describe neuron development in vitro and provides a foundation for analyzing directional changes in neurite growth for future studies.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10775292","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":"Review Paper: Reporting Practices for Task fMRI Studies.","authors":"Freya Acar,&nbsp;Camille Maumet,&nbsp;Talia Heuten,&nbsp;Maya Vervoort,&nbsp;Han Bossier,&nbsp;Ruth Seurinck,&nbsp;Beatrijs Moerkerke","doi":"10.1007/s12021-022-09606-2","DOIUrl":"https://doi.org/10.1007/s12021-022-09606-2","url":null,"abstract":"<p><p>What are the standards for the reporting methods and results of fMRI studies, and how have they evolved over the years? To answer this question we reviewed 160 papers published between 2004 and 2019. Reporting styles for methods and results of fMRI studies can differ greatly between published studies. However, adequate reporting is essential for the comprehension, replication and reuse of the study (for instance in a meta-analysis). To aid authors in reporting the methods and results of their task-based fMRI study the COBIDAS report was published in 2016, which provides researchers with clear guidelines on how to report the design, acquisition, preprocessing, statistical analysis and results (including data sharing) of fMRI studies (Nichols et al. in Best Practices in Data Analysis and Sharing in Neuroimaging using fMRI, 2016). In the past reviews have been published that evaluate how fMRI methods are reported based on the 2008 guidelines, but they did not focus on how task based fMRI results are reported. This review updates reporting practices of fMRI methods, and adds an extra focus on how fMRI results are reported. We discuss reporting practices about the design stage, specific participant characteristics, scanner characteristics, data processing methods, data analysis methods and reported results.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10776587","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":"Deep Learning Classification of Treatment Response in Diabetic Painful Neuropathy: A Combined Machine Learning and Magnetic Resonance Neuroimaging Methodological Study.","authors":"Kevin Teh,&nbsp;Paul Armitage,&nbsp;Solomon Tesfaye,&nbsp;Dinesh Selvarajah","doi":"10.1007/s12021-022-09603-5","DOIUrl":"https://doi.org/10.1007/s12021-022-09603-5","url":null,"abstract":"<p><p>Functional magnetic resonance imaging (fMRI) has been shown successfully to assess and stratify patients with painful diabetic peripheral neuropathy (pDPN). This supports the idea of using neuroimaging as a mechanism-based technique to individualise therapy for patients with painful DPN. The aim of this study was to use deep learning to predict treatment response in patients with pDPN using resting state functional imaging (rs-fMRI). We divided 43 painful pDPN patients into responders and non-responders to lidocaine treatment (responders n = 29 and non-responders n = 14). We used rs-fMRI to extract functional connectivity features, using group independent component analysis (gICA), and performed automated treatment response deep learning classification with three-dimensional convolutional neural networks (3D-CNN). Using gICA we achieved an area under the receiver operating characteristic curve (AUC) of 96.60% and F1-Score of 95% in a ten-fold cross validation (CV) experiment using our described 3D-CNN algorithm. To our knowledge, this is the first study utilising deep learning methods to classify treatment response in pDPN.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9931783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9338843","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":"Brain Age Prediction in Developing Childhood with Multimodal Magnetic Resonance Images.","authors":"Hongjie Cai,&nbsp;Aojie Li,&nbsp;Guangjun Yu,&nbsp;Xiujun Yang,&nbsp;Manhua Liu","doi":"10.1007/s12021-022-09596-1","DOIUrl":"https://doi.org/10.1007/s12021-022-09596-1","url":null,"abstract":"<p><p>It is well known that brain development is very fast and complex in the early childhood with age-based neurological and physiological changes of brain structure and function. The brain maturity is an important indicator for evaluating the normal development of children. In this paper, we propose a multimodal regression framework to combine the features from structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI) data for age prediction of children. First, three types of features are extracted from sMRI and DTI data. Second, we propose to combine the sparse coding and Q-Learning for feature selection from each modality. Finally, the ensemble regression is performed by random forest based on proximity measures to fuse multimodal features for age prediction. The proposed method is evaluated on 212 participants, including 76 young children less than 2 years old and 136 children aged from 2-15 years old recruited from Shanghai Children's Hospital. The results show that integrating multimodal features has achieved the highest accuracies with the root mean squared error (RMSE) of 0.208 years and mean absolute error (MAE) of 0.150 years for age prediction of young children (0-2), and RMSE of 1.666 years and MAE of 1.087 years for older children (2-15). We have shown that the selected features by Q-Learning can consistently improve the prediction accuracy. The comparison of prediction results demonstrates that the proposed method performs better than other competing methods.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10780896","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":"EBRAINS Live Papers - Interactive Resource Sheets for Computational Studies in Neuroscience.","authors":"Shailesh Appukuttan,&nbsp;Luca L Bologna,&nbsp;Felix Schürmann,&nbsp;Michele Migliore,&nbsp;Andrew P Davison","doi":"10.1007/s12021-022-09598-z","DOIUrl":"https://doi.org/10.1007/s12021-022-09598-z","url":null,"abstract":"<p><p>We present here an online platform for sharing resources underlying publications in neuroscience. It enables authors to easily upload and distribute digital resources, such as data, code, and notebooks, in a structured and systematic way. Interactivity is a prominent feature of the Live Papers, with features to download, visualise or simulate data, models and results presented in the corresponding publications. The resources are hosted on reliable data storage servers to ensure long term availability and easy accessibility. All data are managed via the EBRAINS Knowledge Graph, thereby helping maintain data provenance, and enabling tight integration with tools and services offered under the EBRAINS ecosystem.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9931781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10775282","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":"Dementia in Convolutional Neural Networks: Using Deep Learning Models to Simulate Neurodegeneration of the Visual System.","authors":"Jasmine A Moore,&nbsp;Anup Tuladhar,&nbsp;Zahinoor Ismail,&nbsp;Pauline Mouches,&nbsp;Matthias Wilms,&nbsp;Nils D Forkert","doi":"10.1007/s12021-022-09602-6","DOIUrl":"https://doi.org/10.1007/s12021-022-09602-6","url":null,"abstract":"<p><p>Although current research aims to improve deep learning networks by applying knowledge about the healthy human brain and vice versa, the potential of using such networks to model and study neurodegenerative diseases remains largely unexplored. In this work, we present an in-depth feasibility study modeling progressive dementia in silico with deep convolutional neural networks. Therefore, networks were trained to perform visual object recognition and then progressively injured by applying neuronal as well as synaptic injury. After each iteration of injury, network object recognition accuracy, saliency map similarity between the intact and injured networks, and internal activations of the degenerating models were evaluated. The evaluation revealed that cognitive function of the network progressively decreased with increasing injury load whereas this effect was much more pronounced for synaptic damage. The effects of neurodegeneration found for the in silico model are especially similar to the loss of visual cognition seen in patients with posterior cortical atrophy.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10772103","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":"An Algorithm Based on a Cable-Nernst Planck Model Predicting Synaptic Activity throughout the Dendritic Arbor with Micron Specificity.","authors":"Claire Guerrier,&nbsp;Tristan Dellazizzo Toth,&nbsp;Nicolas Galtier,&nbsp;Kurt Haas","doi":"10.1007/s12021-022-09609-z","DOIUrl":"https://doi.org/10.1007/s12021-022-09609-z","url":null,"abstract":"<p><p>Recent technological advances have enabled the recording of neurons in intact circuits with a high spatial and temporal resolution, creating the need for modeling with the same precision. In particular, the development of ultra-fast two-photon microscopy combined with fluorescence-based genetically-encoded Ca²⁺-indicators allows capture of full-dendritic arbor and somatic responses associated with synaptic input and action potential output. The complexity of dendritic arbor structures and distributed patterns of activity over time results in the generation of incredibly rich 4D datasets that are challenging to analyze (Sakaki et al. in Frontiers in Neural Circuits 14:33, 2020). Interpreting neural activity from fluorescence-based Ca²⁺ biosensors is challenging due to non-linear interactions between several factors influencing intracellular calcium ion concentration and its binding to sensors, including the ionic dynamics driven by diffusion, electrical gradients and voltage-gated conductances. To investigate those dynamics, we designed a model based on a Cable-like equation coupled to the Nernst-Planck equations for ionic fluxes in electrolytes. We employ this model to simulate signal propagation and ionic electrodiffusion across a dendritic arbor. Using these simulation results, we then designed an algorithm to detect synapses from Ca²⁺ imaging datasets. We finally apply this algorithm to experimental Ca²⁺-indicator datasets from neurons expressing jGCaMP7s (Dana et al. in Nature Methods 16:649-657, 2019), using full-dendritic arbor sampling in vivo in the Xenopus laevis optic tectum using fast random-access two-photon microscopy. Our model reproduces the dynamics of visual stimulus-evoked jGCaMP7s-mediated calcium signals observed experimentally, and the resulting algorithm allows prediction of the location of synapses across the dendritic arbor. Our study provides a way to predict synaptic activity and location on dendritic arbors, from fluorescence data in the full dendritic arbor of a neuron recorded in the intact and awake developing vertebrate brain.</p>","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10833873","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}