Journal of Neuroscience Methods最新文献

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Chronic recording of brain activity in awake toads 清醒蟾蜍大脑活动的慢性记录
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-18 DOI: 10.1016/j.jneumeth.2025.110449
Daniel A. Shaykevich , Grace A. Woods , Lauren A. O’Connell , Guosong Hong
{"title":"Chronic recording of brain activity in awake toads","authors":"Daniel A. Shaykevich ,&nbsp;Grace A. Woods ,&nbsp;Lauren A. O’Connell ,&nbsp;Guosong Hong","doi":"10.1016/j.jneumeth.2025.110449","DOIUrl":"10.1016/j.jneumeth.2025.110449","url":null,"abstract":"<div><h3>Background</h3><div>Amphibians represent an important evolutionary transition from aquatic to terrestrial environments and they display a large variety of complex behaviors despite a relatively simple brain. However, their brain activity is not as well characterized as that of many other vertebrates, partially due to physiological traits that have made electrophysiology recordings difficult to perform in awake and moving animals.</div></div><div><h3>New method</h3><div>We implanted flexible mesh electronics in the cane toad (<em>Rhinella marina</em>) and performed extracellular recordings in the telencephalon of anesthetized toads and awake toads over multiple days.</div></div><div><h3>Results</h3><div>Though we struggled with maintaining implants in all operated animals, we recorded brain activity over five consecutive days in 5 awake toads and over a 15 week period in a toad that was anesthetized during recordings. We were able to perform spike sorting and identified single- and multi-unit activity in all toads.</div></div><div><h3>Comparison with existing methods</h3><div>To our knowledge, this is the first report of a modern method to perform electrophysiology in non-paralyzed toads over multiple days, though there are historical references to short term recordings in the past.</div></div><div><h3>Conclusions</h3><div>Optimizing flexible mesh electronics in amphibian species will allow for advanced studies of the neural basis of amphibian behaviors.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"419 ","pages":"Article 110449"},"PeriodicalIF":2.7,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852293","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}
引用次数: 0
Unsupervised alignment in neuroscience: Introducing a toolbox for Gromov–Wasserstein optimal transport 神经科学中的无监督对齐:介绍Gromov-Wasserstein最优传输的工具箱
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-14 DOI: 10.1016/j.jneumeth.2025.110443
Ken Takeda , Masaru Sasaki , Kota Abe, Masafumi Oizumi
{"title":"Unsupervised alignment in neuroscience: Introducing a toolbox for Gromov–Wasserstein optimal transport","authors":"Ken Takeda ,&nbsp;Masaru Sasaki ,&nbsp;Kota Abe,&nbsp;Masafumi Oizumi","doi":"10.1016/j.jneumeth.2025.110443","DOIUrl":"10.1016/j.jneumeth.2025.110443","url":null,"abstract":"<div><h3>Background:</h3><div>Understanding how sensory stimuli are represented across different brains, species, and artificial neural networks is a critical topic in neuroscience. Traditional methods for comparing these representations typically rely on supervised alignment, which assumes direct correspondence between stimuli representations across brains or models. However, it has limitations when this assumption is not valid, or when validating the assumption itself is the goal of the research.</div></div><div><h3>New method:</h3><div>To address the limitations of supervised alignment, we propose an unsupervised alignment method based on Gromov–Wasserstein optimal transport (GWOT). GWOT optimally identifies correspondences between representations by leveraging internal relationships without external labels, revealing intricate structural correspondences such as one-to-one, group-to-group, and shifted mappings.</div></div><div><h3>Results:</h3><div>We provide a comprehensive methodological guide and introduce a toolbox called GWTune for using GWOT in neuroscience. Our results show that GWOT can reveal detailed structural distinctions that supervised methods may overlook. We also demonstrate successful unsupervised alignment in key data domains, including behavioral data, neural activity recordings, and artificial neural network models, demonstrating its flexibility and broad applicability.</div></div><div><h3>Comparison with existing methods:</h3><div>Unlike traditional supervised alignment methods such as Representational Similarity Analysis, which assume direct correspondence between stimuli, GWOT provides a nuanced approach that can handle different types of structural correspondence, including fine-grained and coarse correspondences. Our method would provide richer insights into the similarity or difference of representations by revealing finer structural differences.</div></div><div><h3>Conclusion:</h3><div>We anticipate that our work will significantly broaden the accessibility and application of unsupervised alignment in neuroscience, offering novel perspectives on complex representational structures. By providing a user-friendly toolbox and a detailed tutorial, we aim to facilitate the adoption of unsupervised alignment techniques, enabling researchers to achieve a deeper understanding of cross-brain and cross-species representation analysis.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"419 ","pages":"Article 110443"},"PeriodicalIF":2.7,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143860024","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}
引用次数: 0
Detailed characterization of partial tumor resection in the Syngeneic Fischer/F98 Glioma Model 同基因Fischer/F98胶质瘤模型中部分肿瘤切除的详细特征
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-11 DOI: 10.1016/j.jneumeth.2025.110447
Laurence Déry , Gabriel Charest , Brigitte Guérin , David Fortin
{"title":"Detailed characterization of partial tumor resection in the Syngeneic Fischer/F98 Glioma Model","authors":"Laurence Déry ,&nbsp;Gabriel Charest ,&nbsp;Brigitte Guérin ,&nbsp;David Fortin","doi":"10.1016/j.jneumeth.2025.110447","DOIUrl":"10.1016/j.jneumeth.2025.110447","url":null,"abstract":"<div><h3>Background</h3><div>Preclinical models of brain tumors play a fundamental role in understanding tumor biology and deploying anti-tumor strategies. However, preclinical studies evaluate their potential therapy in tumor model without prior resection. Nevertheless, maximal safe resection, the first step in the clinical treatment of glioblastoma (GBM), is known to have a significant effect on adjuvant treatments.</div></div><div><h3>New method</h3><div>We have therefore characterized two techniques to perform tumor resection in F98 glioma-bearing rats to bring this model closer to the clinical context. A total of 65 animals were assigned in 5 different groups: control, catheter (1.74 mm diameter) and biopsy punch (1.5/ 2.5/ 3 mm diameter). On day 10 post-tumor implantation, some animals were sacrificed on day 11 for histological analysis whereas the remaining animals were used for survival estimates.</div></div><div><h3>Results</h3><div>All animals in the survival groups that underwent tumor resection recurred. The resection cavities were visible on the H&amp;E histological sections. No significant difference was observed between the control and resection groups in term of survival but there was a trend towards improved survival with increasing tool diameter.</div></div><div><h3>Comparison with existing methods</h3><div>Few studies have investigated the development of tumor resection models, but the majority of these techniques require sophisticated equipment. To our knowledge, we are the first to develop an easy-to-perform partial tumour resection model using the Fischer-F98 glioma model.</div></div><div><h3>Conclusions</h3><div>Here we present a detailed characterization of the tumor resection procedure and recurrence model, which has potential for the investigation of local delivery strategies in the treatment of GBM.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"418 ","pages":"Article 110447"},"PeriodicalIF":2.7,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143826432","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}
引用次数: 0
Precisely-timed outpatient recordings of subcortical local field potentials from wireless streaming-capable deep-brain stimulators: a method and toolbox 精确定时门诊记录的皮质下局部场电位从无线流能力的脑深部刺激器:一种方法和工具箱
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-11 DOI: 10.1016/j.jneumeth.2025.110448
Cheol Soh , Mario Hervault , Andrea H. Rohl , Jeremy D.W. Greenlee , Jan R. Wessel
{"title":"Precisely-timed outpatient recordings of subcortical local field potentials from wireless streaming-capable deep-brain stimulators: a method and toolbox","authors":"Cheol Soh ,&nbsp;Mario Hervault ,&nbsp;Andrea H. Rohl ,&nbsp;Jeremy D.W. Greenlee ,&nbsp;Jan R. Wessel","doi":"10.1016/j.jneumeth.2025.110448","DOIUrl":"10.1016/j.jneumeth.2025.110448","url":null,"abstract":"<div><h3>Background</h3><div>Investigations of the electrophysiological mechanisms of the human subcortex have relied on recording local field potentials (LFPs) during deep-brain stimulation (DBS) neurosurgery. However, the neurosurgical setting severely restricts the research use of these recordings. Recently developed sensing-capable DBS devices wirelessly stream subcortical LFPs in outpatient settings. These recordings have tremendous potential for research. However, synchronizing them with other behavior or neural recordings is challenging, as the clinical devices do not accept digital timing information.</div></div><div><h3>New method</h3><div>Switching the DBS device on introduces transient yet consistent artifacts in both the LFP and simultaneous scalp-EEG recordings. We use these artifacts as a reference to align these recordings (N = 20). We tested whether the alignment was precise enough to match a ground truth state (large artifacts produced by transcranial magnetic stimulation, TMS), yielded trial-averaged event-locked LFPs, and phase consistency across trials. We further evaluated the consistency of task-related LFPs across outpatient and perisurgical recordings.</div></div><div><h3>Results and comparison with existing method(s)</h3><div>Previous alignment methods were limited because they relied on inconsistent on/offset features of DBS artifacts caused by ongoing stimulation. Moreover, they only provided limited validation. Our highly precise alignment method showed a maximum deviation of only 8 ms – clearly superior to prior techniques. Furthermore, event-related activity patterns were comparable across outpatient and perisurgical LFP recordings.</div></div><div><h3>Conclusions</h3><div>We present a method and a MATLAB toolbox that inserts the most precise digital timing information into wirelessly-streamed DBS-LFP recordings to date. By enabling event-related research with high-temporal precision, this method greatly enhances the utility of these recordings.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"418 ","pages":"Article 110448"},"PeriodicalIF":2.7,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143829650","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}
引用次数: 0
μGlia-Flow, an automatic workflow for microglia segmentation and classification μGlia-Flow,一种用于小胶质细胞分割和分类的自动工作流
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-10 DOI: 10.1016/j.jneumeth.2025.110446
Huangrui Xiong , Siling Zheng , Xiuhong Qi , Ji Liu
{"title":"μGlia-Flow, an automatic workflow for microglia segmentation and classification","authors":"Huangrui Xiong ,&nbsp;Siling Zheng ,&nbsp;Xiuhong Qi ,&nbsp;Ji Liu","doi":"10.1016/j.jneumeth.2025.110446","DOIUrl":"10.1016/j.jneumeth.2025.110446","url":null,"abstract":"<div><h3>Background</h3><div>Microglia are important immune cells in the central nervous system, playing a key role in various pathological processes. The morphological diversity of microglia is closely linked to the development of brain diseases, yet accurate segmentation and automatic classification of microglia remain challenging.</div></div><div><h3>New method</h3><div>We proposed a workflow, μGlia-Flow, which integrates both segmentation and classification for microglia analysis. The Frangi filtering algorithm was employed for branch segmentation, and an edge-guided attention TransUNet (EGA-Net) was used for soma segmentation. A Vision Transformer (ViT) network was applied to classify different morphologies.</div></div><div><h3>Results</h3><div>The Frangi filtering algorithm produces more complete branches with smoother edges and clearer structures. The EGA-Net improves Dice and IoU scores by 4.02 % and 6.75 %, respectively. ViT achieves over 99 % precision in classification. Post-processing reveals decreasing complexity during activation, validating the accuracy of μGlia-Flow.</div></div><div><h3>Comparison with existing methods</h3><div>μGlia-Flow introduces deep learning, significantly improving segmentation accuracy and addressing the parameter dependency of existing classification methods.</div></div><div><h3>Conclusion</h3><div>we present an automatic workflow for segmenting and classifying microglia, providing a powerful tool for different morphology analysis.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"419 ","pages":"Article 110446"},"PeriodicalIF":2.7,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143830090","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}
引用次数: 0
Multi-day recordings and adaptive stimulation protocols for in-home collection of deep brain stimulation intracranial recordings 多天记录和自适应刺激方案在家庭收集深部脑刺激颅内记录。
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-04 DOI: 10.1016/j.jneumeth.2025.110442
Jonathan P. Platt , Erin M. Radcliffe , Steven L. Klimczak , Stephen V. Gliske , Christopher K. Kovach , Dulce Maroni , Aviva Abosch , John A. Thompson
{"title":"Multi-day recordings and adaptive stimulation protocols for in-home collection of deep brain stimulation intracranial recordings","authors":"Jonathan P. Platt ,&nbsp;Erin M. Radcliffe ,&nbsp;Steven L. Klimczak ,&nbsp;Stephen V. Gliske ,&nbsp;Christopher K. Kovach ,&nbsp;Dulce Maroni ,&nbsp;Aviva Abosch ,&nbsp;John A. Thompson","doi":"10.1016/j.jneumeth.2025.110442","DOIUrl":"10.1016/j.jneumeth.2025.110442","url":null,"abstract":"<div><h3>Background</h3><div>While open-loop deep brain stimulation (DBS) is an effective therapy for the motor symptoms of Parkinson’s Disease (PD), recent work has explored whether closed-loop adaptive DBS (aDBS) may better address fluctuating symptoms through patient-specific and symptom-relevant neurophysiological biomarkers. To aid these investigations, we designed an interface for the research-enabled Summit Medtronic RC+S (RC+S) implanted neurostimulator (INS) to collect multi-day recordings along with the implementation of aDBS therapy.</div></div><div><h3>New method</h3><div>We developed applications in MATLAB for investigating optimal brain recording locations, setting thresholds for real-time analysis, determining the INS’s position along with in-home recordings of neural activity, and implementation of aDBS algorithms.</div></div><div><h3>Results</h3><div>In a pilot study conducted in PD subjects (n = 5), we successfully determined optimal DBS lead contacts for detecting maximal beta (13–30 Hz) activity for streaming in-home neural activity with closed-loop adjustments to stimulation amplitude (n = 24–27 days). Using a Bluetooth connection method we developed, 95.2 % in-home data was collected.</div></div><div><h3>Comparison with existing methods</h3><div>The software and hardware applications described in this report provide MATLAB based tools to enable a distributed strategy for interfacing with the RC+S deployed at in-home settings for multi-hour recordings.</div></div><div><h3>Conclusions</h3><div>Our interface provides investigators using the RC+S, in the context of aDBS, access to chronic recordings in real-time while providing adaptive stimulation based on continuous data analysis in MATLAB using a USB or Bluetooth connection. Advancing the efforts to characterize relevant biomarkers and develop therapeutic aDBS strategies for those treated with DBS, such as PD.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"418 ","pages":"Article 110442"},"PeriodicalIF":2.7,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795716","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}
引用次数: 0
Adaptations to the neuronal culture for researchers at undergraduate institutions 本科院校研究人员对神经元培养的适应。
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-03 DOI: 10.1016/j.jneumeth.2025.110437
Briahna Galvan, Taranjot Singh, Prajwal Kurup, Jake Alvarez, Atta Bettagi, Henry Stewart, Anuraj Nair, Szilard Menes, Meera Patel, Jary Y. Delgado
{"title":"Adaptations to the neuronal culture for researchers at undergraduate institutions","authors":"Briahna Galvan,&nbsp;Taranjot Singh,&nbsp;Prajwal Kurup,&nbsp;Jake Alvarez,&nbsp;Atta Bettagi,&nbsp;Henry Stewart,&nbsp;Anuraj Nair,&nbsp;Szilard Menes,&nbsp;Meera Patel,&nbsp;Jary Y. Delgado","doi":"10.1016/j.jneumeth.2025.110437","DOIUrl":"10.1016/j.jneumeth.2025.110437","url":null,"abstract":"<div><h3>Background</h3><div>The use of rat hippocampal neurons in culture has become an essential tool in neuroscience, enabling detailed study of excitatory synapse organization, neurotransmitter release, and mechanisms of synaptic plasticity. While these cultures provide valuable insights, the physiological relevance of this simplified in vitro system remains an ongoing discussion. Research indicates that cultured hippocampal neurons undergo key maturation processes, including the development of mature dendritic spines, within weeks, mirroring aspects of in vivo development. Importantly, cultured neurons offer unique experimental flexibility, facilitating single-neuron manipulations that is technically challenging or impractical in intact brain slices or with viral vectors. Despite these advantages, establishing cultures with minimal glial support—critical for experiments involving sparse labeling of extracellular proteins for single-particle tracking—often demands substantial time, expertise, and resources, making it difficult to implement in smaller laboratories with limited personnel and funding.</div></div><div><h3>New method</h3><div>In this study, we present modifications to the standard hippocampal culture protocol designed to improve accessibility and usability in resource-limited settings, such as undergraduate-focused institutions.</div></div><div><h3>Results/Comparison</h3><div>Our protocol reduces costs, simplifies the culturing process, and minimizes time requirements, supporting robust neuronal cultures with physiological properties comparable to those of traditional methods. These adaptations enable the execution of sophisticated experiments, including single-molecule tracking, in personnel-limited research environments.</div></div><div><h3>Conclusions</h3><div>This approach highlights the potential for undergraduate institutions to make significant contributions to scientific advancements, rather than being viewed solely as centers for undergraduate training.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"418 ","pages":"Article 110437"},"PeriodicalIF":2.7,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788411","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}
引用次数: 0
Determining the atlas correspondence of Desikan-Killiany-Tourville and Glasser MMP1 atlases across magnetic field strengths 确定desikan - killian - tourville和Glasser MMP1地图集在磁场强度上的对应关系。
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-03 DOI: 10.1016/j.jneumeth.2025.110445
Madison Lewis , Nicholas Theis , Nidhi Girish , Konasale Prasad
{"title":"Determining the atlas correspondence of Desikan-Killiany-Tourville and Glasser MMP1 atlases across magnetic field strengths","authors":"Madison Lewis ,&nbsp;Nicholas Theis ,&nbsp;Nidhi Girish ,&nbsp;Konasale Prasad","doi":"10.1016/j.jneumeth.2025.110445","DOIUrl":"10.1016/j.jneumeth.2025.110445","url":null,"abstract":"<div><h3>Background</h3><div>Over sixty-six brain atlases exist to parcellate the brain based on cytoarchitecture, function, and connectivity. Because atlas choice depends on individual study goals and hypotheses, variability in findings contributes to challenges in replication, validation, and reconciling the results across studies. Our goal was to measure the intersection of three commonly used atlases and create a tool to find regional correspondence between the atlases.</div></div><div><h3>New method</h3><div>This study used three independent samples of anatomical MRI data acquired with different B0 magnetic field strengths: 1.5 Tesla (T), 3 T, and 7 T. The Desikan-Killiany- Tourville (DKT) and Glasser atlases were used to parcellate the brain. Coefficient-of- variation of regional volumes was measured to evaluate regional variability across subjects in each atlas. DKT and Glasser parcellation correspondence was calculated to answer the shared question of what Glasser regions intersect with a DKT region and vice versa and to investigate consistency of the parcellations in relation to each other across a variety of individuals and image resolutions.</div></div><div><h3>Results</h3><div>We found that regional correspondence was consistent across field strengths for the DKT and Glasser parcellations despite showing population variability in volume, age, and sex, and was validated in the Schaefer400 atlas. Parcellation intersection data along with sample code to calculate specific regional correspondence is available.</div></div><div><h3>Comparison with existing methods</h3><div>Prior studies have attempted to reconcile multiple atlases, but did not compare voxel- by-voxel on real data.</div></div><div><h3>Conclusion</h3><div>This analysis created a tool for researchers and can aid in comparisons with differing atlas choice and variable field strengths.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"418 ","pages":"Article 110445"},"PeriodicalIF":2.7,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788461","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}
引用次数: 0
Neurocounter - A deep learning framework for high-fidelity spatial localization of neurons 神经计数器-一个用于高保真神经元空间定位的深度学习框架。
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-03 DOI: 10.1016/j.jneumeth.2025.110444
Tamal Batabyal , Aijaz Ahmad Naik , Jaideep Kapur
{"title":"Neurocounter - A deep learning framework for high-fidelity spatial localization of neurons","authors":"Tamal Batabyal ,&nbsp;Aijaz Ahmad Naik ,&nbsp;Jaideep Kapur","doi":"10.1016/j.jneumeth.2025.110444","DOIUrl":"10.1016/j.jneumeth.2025.110444","url":null,"abstract":"<div><h3>Background</h3><div>Many neuroscientific applications require robust and accurate localization of neurons. It is still an unsolved problem because of the enormous variation in intensity, texture, spatial overlap, morphology, and background artifacts. In addition, curating a large dataset containing complete manual annotation of neurons from high-resolution images for training a classifier requires significant time and effort. In this work, we presented Neurocounter, a deep learning network to detect and localize neurons.</div></div><div><h3>New method</h3><div>Neurocounter contains an encoder, a decoder and an attention module. It is trained on images containing incompletely-annotated neurons having highly varied morphology, and control images containing artifacts and background structures. During training, Neurocounter progressively labels the un-annotated neurons in the training data. It detects centers of neuron soma as the output.</div></div><div><h3>Results</h3><div>Neurocounter's self-learning ability reduces the need for time-intensive complete annotation and ensures high accuracy in the localization of neurons across various brain regions (approximately 94 % F1 score).</div><div>Comparison with existing methods</div><div>Neurocounter shows its efficacy over the state of the arts by significantly reducing false-positive detection (by at least 3 %).</div></div><div><h3>Conclusions</h3><div>Neurocounter offers precise neuron soma detection in various scenarios, such as with background artifacts, clutter and overlapped cell soma. This tool can be potentially used to reconstruct brain-wide 3D maps of activated neurons from 2D localization of neurons.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"418 ","pages":"Article 110444"},"PeriodicalIF":2.7,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788477","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}
引用次数: 0
Enhancing robustness of spatial filters in motor imagery based brain-computer interface via temporal learning 通过时态学习增强基于运动图像的脑机接口中空间滤波器的鲁棒性
IF 2.7 4区 医学
Journal of Neuroscience Methods Pub Date : 2025-04-02 DOI: 10.1016/j.jneumeth.2025.110441
Wei Liang , Ren Xu , Xingyu Wang , Andrzej Cichocki , Jing Jin
{"title":"Enhancing robustness of spatial filters in motor imagery based brain-computer interface via temporal learning","authors":"Wei Liang ,&nbsp;Ren Xu ,&nbsp;Xingyu Wang ,&nbsp;Andrzej Cichocki ,&nbsp;Jing Jin","doi":"10.1016/j.jneumeth.2025.110441","DOIUrl":"10.1016/j.jneumeth.2025.110441","url":null,"abstract":"<div><h3>Background</h3><div>In motor imagery-based brain-computer interface (MI-BCI) EEG decoding, spatial filtering play a crucial role in feature extraction. Recent studies have emphasized the importance of temporal filtering for extracting discriminative features in MI tasks. While many efforts have been made to optimize feature extraction externally, stabilizing features from spatial filtering remains underexplored.</div><div>New method: To address this problem, we propose an approach to improve the robustness of temporal features by minimizing instability in the temporal domain. Specifically, we utilize Jensen-Shannon divergence to quantify temporal instability and integrate decision variables to construct an objective function that minimizes this instability. Our method enhances the stability of variance and mean values in the extracted features, improving the identification of discriminative features and reducing the effects of instability.</div></div><div><h3>Results</h3><div>The proposed method was applied to spatial filtering models, and tested on two publicly datasets as well as a self-collected dataset. Results demonstrate that the proposed method significantly boosts classification accuracy, confirming its effectiveness in enhancing temporal feature stability.</div><div>Comparison with existing methods: We compared our method with spatial filtering methods, and the-state-of-the-art models. The proposed approach achieves the highest accuracy, with 92.43 % on BCI competition III IVa dataset, 84.45 % on BCI competition IV 2a dataset, and 73.18 % on self-collected dataset.</div></div><div><h3>Conclusions</h3><div>Enhancing the instability of temporal features contributes to improved MI-BCI performance. This not only improves classification performance but also provides a stable foundation for future advancements. The proposed method shows great potential for EEG decoding.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"418 ","pages":"Article 110441"},"PeriodicalIF":2.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780245","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}
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