Journal of neural engineering最新文献

{"title":"An ICA-based artifact suppression method for online extraction of TMS-evoked potentials: toward closed-loop TMS-EEG applications beyond the motor cortex.","authors":"Sina Varmaghani, Ronald Phlypo, Olivier David, Sylvain Harquel, Alan Chauvin","doi":"10.1088/1741-2552/ae01d8","DOIUrl":"10.1088/1741-2552/ae01d8","url":null,"abstract":"<p><p><i>Objective.</i>Transcranial magnetic stimulation (TMS) combined with electroencephalography (EEG) has become a valuable tool in clinical and cognitive neuroscience. However, TMS-EEG signals often suffer from severe artifacts, particularly in lateral cortical regions where TMS-evoked muscle artifacts are pronounced, making real-time recovery of TMS-evoked potentials (TEPs) challenging. We developed and validated a real-time, two-step independent component analysis (ICA)-based artifact cleaning method for TMS-EEG signals, facilitating the rapid extraction of clean neural signals for closed-loop neurostimulation applications.<i>Approach.</i>Our method involves an offline ICA training phase, where ICA weights and artifact topographies are identified using pre-experimental trials, followed by an online phase in which the precomputed weight matrices are applied in real-time to incoming data. We conducted simulations on two pre-published TMS-EEG datasets (<i>N</i>= 28, ROIs = 6) to validate the method by identifying the minimum number of trials required to estimate ICA weights. We also assessed the reproducibility of TEPs and the stability of ICA components, taking classical offline TEPs as the relative ground truth.<i>Main Results.</i>ICA analysis suggests that it can be applied reliably within each region without significant loss of convergence and stability, provided careful consideration is given to the size and composition of the data used for ICA training. Simulation results indicated that while central regions could achieve reliable TEPs similar to ground truth with as few as 20-30 trials to train ICA in the pre-experimental phase, frontal and occipital regions required 50-60 trials to reach a comparable level of reliability. Later TEP peaks (>100 ms) in all regions achieved high reproducibility when at least 35 training trials were used, whereas earlier peaks (<80 ms) showed moderate reproducibility with the same number of trials.<i>Significance.</i>These findings establish the feasibility and proof-of-concept for real-time ICA-based artifact removal for closed-loop TMS-EEG applications. The method enables rapid extraction of clean neural signals, allowing adaptation of stimulation parameters in real time, thereby facilitating individualized neurostimulation paradigms.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144983796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Personalized beta band HD-tACS over the left SMA improves speech and limb movement by modulating prefrontal delta oscillations in neurotypical young adults.","authors":"Fatemeh Tabari, Joel Isaac Berger, Melda Kunduk, Arend W A Van Gemmert, Karim Johari","doi":"10.1088/1741-2552/ae00f5","DOIUrl":"10.1088/1741-2552/ae00f5","url":null,"abstract":"<p><p><i>Objective</i>. The supplementary motor area (SMA) demonstrates abnormal beta activity (13-30 Hz) during speech and limb movement tasks in neurological conditions such as Parkinson's disease (PD). Transcranial alternating current stimulation (tACS) has demonstrated promising improvement in motor and non-motor functions by entraining endogenous neural oscillations. We conducted an exploratory study on the modulatory effects of personalized beta high-definition (HD)-tACS over the left SMA on speech production and limb movement.<i>Approach.</i>In a repeated-measures experiment, twenty-two neurotypical young adults were recruited to participate in four stimulation conditions: sham, HD transcranial random noise stimulation (HD-tRNS), and HD-tACS tuned to each individual's frequency of maximal SMA beta activity (identified using source-localized EEG) during speech (tuned-to-speech, TtS) and limb movement (tuned-to-limb, TtL). All participants completed a 25 min sham/active stimulation over the left SMA, followed by an interleaved speech production and limb movement task.<i>Main results</i>. Behavioral results showed that active stimulation resulted in more pronounced improvements in reaction times compared to the sham condition, regardless of the active stimulation type. The neural correlates of this aftereffect were indicated by a prominent modulation in delta power in prefrontal and frontocentral electrodes during speech and limb movement tasks following personalized beta TtS and TtL HD-tACS, relative to sham and tRNS.<i>Significance</i>. Personalized beta HD-tACS modulated delta oscillations, rather than beta rhythms, in a task-specific manner, highlighting the brain's adaptive response. These findings have implications for neurological conditions such as PD, which are characterized by deficits in speech production and limb motor coordination.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144984119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inhibiting JNK and PI3K-Akt signaling pathways altered spontaneous network bursts and developmental trajectories of neuronal networks.","authors":"Xiaoli Jia, Qiuyan Zhu, Hailin Lu, Zhihong Zhou, Tahir Ali, Shupeng Li, Jinxing Feng","doi":"10.1088/1741-2552/ae01db","DOIUrl":"10.1088/1741-2552/ae01db","url":null,"abstract":"<p><p><i>Objective.</i>Spontaneous network bursts (NBs) are critical for neuronal circuit development, influencing synaptogenesis and functional organization. While JNK and PI3K-Akt signaling pathways are known to regulate synaptic plasticity, their specific roles in governing NBs dynamics and functional network organization remain poorly understood. This study investigates the roles of JNK and PI3K-Akt signaling in regulating spontaneous NBs dynamics and network organization in cultured neuronal networks.<i>Approach.</i>Using longitudinal microelectrode array (MEA) recordings from cultured cortical neurons (DIV14-49), we pharmacologically inhibited JNK (SP600125, JNK-IN-8) and PI3K-Akt (LY294002, GDC-0941) pathways. We quantitatively analyzed NBs profiles (maximum firing rate/MFR, burst length/BL, rising phase/RP) and functional network properties (modularity, betweenness centrality) during development.<i>Main results.</i>JNK inhibition increased MFR but reduced RP and FP, and decreased betweenness centrality and network modularity, particularly in DIV21. PI3K-Akt inhibition caused delayed effects: decreased MFR at DIV49 with increased RP, while enhancing network modularity. Developmental analysis revealed a transition from core-node-driven NBs (strong MFR-betweenness and BL-betweenness correlation at DIV14) to modularly organized NBs (strong BL-modularity and MFR-modularity correlation at DIV49), with pathway inhibitors differentially altering these relationships.<i>Significance.</i>Our findings demonstrate that JNK and PI3K-Akt pathways play distinct temporal roles in regulating NBs dynamics and network organization. JNK signaling is crucial for maintaining early core-node functionality, whereas PI3K-Akt signaling promotes the development of mature modular architecture. Our findings enhance the understanding of how molecular signaling influences neuronal network dynamics, contributing to a broader framework for studying neurodevelopmental principles.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144983793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The speech reception threshold can be estimated using EEG electrodes in and around the ear.","authors":"Heidi B Borges, Johannes Zaar, Emina Alickovic, Christian B Christensen, Preben Kidmose","doi":"10.1088/1741-2552/ae00f3","DOIUrl":"10.1088/1741-2552/ae00f3","url":null,"abstract":"<p><p><i>Objective.</i>Previous studies have demonstrated that the speech reception threshold (SRT) can be estimated using scalp electroencephalography (EEG), referred to as SRT_neuro. The present study assesses the feasibility of using ear-EEG, which allows for discreet measurement of neural activity from in and around the ear, to estimate the SRT_neuro.<i>Approach.</i>Twenty young normal-hearing participants listened to audiobook excerpts at varying signal-to-noise ratios (SNRs) whilst wearing a 66-channel EEG cap and 12 ear-EEG electrodes. A linear decoder was trained on different electrode configurations to estimate the envelope of the audio excerpts from the EEG recordings. The reconstruction accuracy was determined by calculating the Pearson's correlation between the actual and the estimated envelope. A sigmoid function was then fitted to the reconstruction-accuracy-vs-SNR data points, with the midpoint of the sigmoid serving as the SRT_neuroestimate for each participant.<i>Main results.</i>Using only in-ear electrodes, the estimated SRT_neurowas within 3 dB of the behaviorally measured SRT (SRT_beh) for 6 out of 20 participants (30%). With electrodes placed both in and around the ear, the SRT_neurowas within 3 dB of the SRT_behfor 19 out of 20 participants (95%) and thus on par with the reference estimate obtained from full-scalp EEG. Using only electrodes in and around the ear from the right side of the head, the SRT_neuroremained within 3 dB of the SRT_behfor 19 out of 20 participants.<i>Significance.</i>These findings suggest that the SRT_neurocan be reliably estimated using ear-EEG, especially when combining in-ear electrodes and around-the-ear electrodes. Such an estimate can be highly useful e.g. for continuously adjusting noise-reduction algorithms in hearing aids or for logging the SRT in the user's natural environment.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144984083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Amorphous silicon resistors enable smaller pixels in photovoltaic retinal prosthesis.","authors":"Andrew Shin, Nathan Jensen, Emma Butt, Jeonghyun An, Davis Pham-Howard, Ludwig Galambos, Keith Mathieson, Theodore Kamins, Daniel Palanker","doi":"10.1088/1741-2552/ae0522","DOIUrl":"https://doi.org/10.1088/1741-2552/ae0522","url":null,"abstract":"<p><strong>Objective: </strong>Clinical trials of the photovoltaic subretinal prosthesis PRIMA demonstrated feasibility of prosthetic central vision with resolution matching its 100 μm pixel width. To improve prosthetic acuity further, pixel size should be decreased. However, there are multiple challenges, one of which is related to accommodating a compact shunt resistor within each pixel that discharges the electrodes between stimulation pulses and helps increase the contrast of the electric field pattern. Unfortunately, standard materials used in integrated circuit resistors do not match the resistivity required for small photovoltaic pixels. Therefore, we used a novel material - doped amorphous silicon (a-Si) and integrated it into photovoltaic arrays with pixel sizes down to 20 μm.&#xD;Approach. To fit within a few μm²area of the pixels and provide resistance in the MΩ range, the material should have sheet resistance of a few hundred kΩ/sq, which translates to resistivity of a few Ω*cm. The a-Si layer was deposited by low-pressure chemical vapor deposition (LPCVD) and its resistivity was adjusted by PH₃ doping before encapsulating the resistors between SiO₂ and SiC for stability in-vivo.&#xD;Main Results. High-resolution retinal implants with integrated shunt resistors were fabricated with values ranging from 0.75 to 4 MΩ on top of the photovoltaic pixels of 55, 40, 30 and 20 μm in size. Photoresponsivity with all pixel sizes was approximately 0.53 A/W, as high as in the arrays with no shunt resistor. The shunts shortened electrodes discharge time, with the average electric potential in electrolyte decreasing by only 21-31% when repetition rate increased from 2 to 30 Hz, as opposed to a 54-55% decrease without a shunt. Similarly, contrast of a Landolt C pattern increased from 16-22% with no shunt to 22-34% with a shunt. Further improvement in contrast is expected with pillar electrodes and local returns within each pixel.&#xD;Significance. Miniature shunt resistors in a MOhm range can be fabricated from doped a-Si in a process compatible with manufacturing of photovoltaic arrays. The shunt resistors improved current injection and spatial contrast at video frame rates, without compromising the photoresponsivity. These advances are critical for scaling pixel sizes below 100 µm to improve visual acuity of prosthetic vision.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145031507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inter-ictal spike rates are not modulated by anti-seizure medication taper in the epilepsy monitoring unit: a tale of two confounders.","authors":"Nina Jasmine Ghosn, Katherine Walsh, Kevin Xie, Carlos Aguila, Akash Pattnaik, Devin Ma, Abba Krieger, Erin Conrad, Brian Litt","doi":"10.1088/1741-2552/ae0521","DOIUrl":"https://doi.org/10.1088/1741-2552/ae0521","url":null,"abstract":"<p><strong>Objective: </strong>New implantable and wearable devices hold great promise to help patients manage their seizure disorders. One proposed application is measuring the rate of interictal epileptiform discharges as a biomarker of medication levels and seizure risk. This study aims to determine whether interictal epileptiform spike rates (spikes) are independently associated with anti-seizure medication (ASM) levels and evaluate whether spike rates are a reliable biomarker for ASM levels. &#xD;Approach. We conducted a retrospective analysis of 69 patients with drug resistant epilepsy undergoing intracranial EEG monitoring during ASM taper in the Epilepsy Monitoring Unit (EMU). An automated spike detection algorithm, validated seizure annotations, and a model of ASM load were used to assess the relationship between spike rates, ASM level, state of consciousness, and seizure timing using linear mixed effects models. Event related analysis and seasonal autoregressive models were applied to evaluate both short-term and longer-term effects of ASMs on spike rates, respectively.&#xD;Main results. Spike rates were found to increase following seizures, during sleep, and in patients experiencing early seizures, with no significant association between ASM load and spike rates after controlling for these confounders. Initial models without controls showed a positive association between ASM load and spike rates. However, this relationship disappeared when the effects of sleep and seizures were accounted for. Medication-specific analysis revealed that only levetiracetam showed a significant impact on spike rates during taper.&#xD;Significance. This study demonstrates that interictal spike rates are more strongly influenced by seizure activity and sleep than by ASM levels, suggesting limited utility of spike rates as a biomarker for ASM load. However, spikes may still serve as important markers for seizure control and disease severity.&#xD;Key points:&#xD;● Interictal spike rates do not track ASM levels consistently. &#xD;● Spikes are more indicative of seizure activity and sleep than of changing ASM levels.&#xD;● Spikes may still aid in assessing disease severity and epilepsy management, particularly in relation to seizure activity.&#xD.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145031532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic Review of Experimental Studies in Humans on Transcranial Temporal Interference Stimulation.","authors":"Paria Mansourinezhad, R M C Mestrom, Deborah C W Klooster, Mathieu Sprengers, Paul A J M Boon, Maarten M Paulides","doi":"10.1088/1741-2552/ae0524","DOIUrl":"https://doi.org/10.1088/1741-2552/ae0524","url":null,"abstract":"<p><p>Transcranial temporal interference stimulation (tTIS) has recently emerged as a non-invasive neuromodulation method aimed at reaching deeper brain regions than conventional techniques. However, many questions about its effects remain, requiring further experimental studies. This review consolidates the experimental literature on tTIS's effects in the human brain, clarifies existing evidence, identifies knowledge gaps, and proposes future research directions to evaluate its potential. A systematic literature search was performed in PubMed, Web of Science, and Scopus for studies published up to January 27, 2025. Eligible studies applied tTIS to the human brain and examined its effects on neural, behavioral, and clinical outcomes. Of 127 publications screened, 18 met the inclusion criteria. Studies were analyzed for design, stimulation target, parameters, control conditions, and outcome measures. Included studies exhibited low bias or minor concerns using the Cochrane RoB2 and ROBINS-I tools. Ten studies targeted cortical regions (motor, occipito-parietal, fronto-parietal), and eight probed subcortical sites (striatum, hippocampus, globus pallidus, caudate). Motor-cortex tTIS enhanced motor-network connectivity, though the effect was similar to that of tDCS. Beta-band stimulation envelopes (20 Hz) promoted learning-related plasticity, while gamma-band envelopes (70 Hz) yielded immediate performance improvements. Occipito-parietal tTIS did not modulate alpha power. Preliminary deep-target findings are promising: 5 Hz hippocampal tTIS improved episodic recall, 100 Hz striatal tTIS enhanced motor learning in older adults, and 100 Hz hippocampal-entorhinal tTIS aided spatial navigation. Two fMRI studies confirmed network-specific modulation, although one raised concerns about using a fixed montage between individuals. Clinical evidence remains limited, with two Parkinson's pilots and one epilepsy study showing short-term benefits. Overall, tTIS shows potential to modulate human brain activity and behaviour. However, current evidence is preliminary and predominantly focused on cortical rather than deep targets. Larger, well-controlled studies are needed to reliably determine whether tTIS can effectively engage subcortical structures and provide meaningful clinical benefits.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145031567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NaviNIBS: a comprehensive and open-source software toolbox for neuronavigated noninvasive brain stimulation.","authors":"Christopher C Cline, Lily Forman, Winn Hartford, Jade Truong, Sara Parmigiani, Corey J Keller","doi":"10.1088/1741-2552/adfab2","DOIUrl":"10.1088/1741-2552/adfab2","url":null,"abstract":"<p><p><i>Objective.</i>Image-guided positioning, or neuronavigation, is critical for precise targeting of transcranial magnetic stimulation (TMS) and other noninvasive brain stimulation. However, existing commercial systems have limitations in flexibility and extensibility for research applications.<i>Approach.</i>We present new open-source software for neuronavigated non-invasive brain stimulation (NaviNIBS) that provides comprehensive functionality for TMS experiments. NaviNIBS supports imaging data import, target planning, head registration, real-time tool tracking, and integration with robotic positioning and electrophysiology systems. Key features include flexible target specification, support for multiple tracking hardware options, refined head registration techniques, and an extensible addon system.<i>Main results.</i>We describe the software architecture, core functionality, characterization of tracking performance, and example applications of NaviNIBS.<i>Significance.</i>By implementing NaviNIBS and sharing it with the research community, we aim to facilitate methodological improvements and novel experimental paradigms in noninvasive brain stimulation research.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reconstructing high-resolution visual perceptual images from human intracranial electrocorticography signals.","authors":"Yongjie Deng, Xiaolong Wu, Xin Gao, Weizhong Li, Dingguo Zhang","doi":"10.1088/1741-2552/ae0070","DOIUrl":"10.1088/1741-2552/ae0070","url":null,"abstract":"<p><p><i>Objectives.</i>Reconstruction of visual perception from brain signals has emerged as a promising research topic. Electrocorticography (ECoG) is a kind of high-quality intracranial signal with good spatiotemporal resolution that offers some new opportunities. However, according to our knowledge, there are no studies to reconstruct the perceived images from human ECoG signals at present.<i>Approach.</i>We have conducted the pioneering work and developed a novel pipeline that integrates Talairach coordinate alignment masked autoencoders (TA-MAE) with denoising diffusion probabilistic models. Our approach exploits the spatiotemporal dynamics of human ECoG signals, enabling the restoration of details in high-resolution.<i>Main results.</i>Experiments show that our method outperforms the current state-of-the-art methods in terms of appearance, structure, signal-noise ratio, and semantic consistency. Additionally, our study indicated that unsupervised learning-based signal reconstruction outperforms manually annotated label-guided feature recognition in capturing the low-dimensional representation of brain signals, potentially facilitating the exploration of vision's intrinsic mechanisms.<i>Significance.</i>These results highlight the advantages of unsupervised decoding and provide a generalizable framework for human ECoG-based visual reconstruction.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144984091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling functional heterogeneity in anatomical functional areas: a framework for fine-grained functional connectivity analysis of wide-field calcium imaging data.","authors":"Yunhan Li, Yiwen Xu, Yaqin Liu, Chang'an A Zhan","doi":"10.1088/1741-2552/adff39","DOIUrl":"10.1088/1741-2552/adff39","url":null,"abstract":"<p><p><i>Objective</i>. Conventional functional connectivity (FC) analysis of wide-field calcium imaging (WFCI) data relies on the assumption of homogeneity within predefined anatomical functional areas (FAs), where the signal averaged within each FA serves as the foundation for inter-FA connectivity modeling. However, accumulating evidence suggested significant intra-FA functional heterogeneity with functionally distinct subregions. This study aims to systematically examine the existence of the heterogeneity and the consequences of violating the homogeneity assumption on the FC analysis.<i>Approach</i>. We propose a three-step approach: (1) The spatiotemporal clustering of pixels with similar activity dynamics into functional parcels (FPs). (2) Classifying FPs according to their cortex-wide connectivity profiles into four categories: cross-hemispheric (CH), unihemispheric (UH), cross-modal (CM) and unimodal (UM). (3) Gauging the consequences and utility of above analysis.<i>Main results</i>. Analysis of adult mice WFCI data (<i>n</i>= 6) shows that pixels can be reliably clustered into FPs, and that FPs fall into different categories and form distinct subregions, unveiling the functional heterogeneity within each FA. Crucially, fine-grained FC analysis for different categories of subregions uncovered significant differences compared to the results from the conventional method. Application of the analysis to longitudinal WFCI data on mouse brain development (<i>n</i>= 17) demonstrates increases in CM and CH subregions and decreases in UM and UH subregions over time, in line with expectations based on prior research into neurodevelopment and network reorganization.<i>Significance</i>. The present study develops a fine-grained FC analysis framework, leveraging the high spatiotemporal resolution of WFCI to more precisely characterize large-scale cortical network dynamics. The observed differences between FCs derived using the proposed framework and those from conventional methods highlight the need for caution regarding the functional homogeneity assumption in conventional FC analysis. Furthermore, the developmental regularities revealed in longitudinal mouse brain data demonstrate the utility of fine-grained FC analysis.</p>","PeriodicalId":94096,"journal":{"name":"Journal of neural engineering","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144984141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}