Frontiers in Neuroinformatics

Neurophysiology datasets are becoming increasingly complex, combining behavioral measurements with high-dimensional neuronal activity recordings coming from optical and/or electrophysiological measurements. The Neurodata Without Borders (NWB) standard has emerged in the community as the format of record. While standardized and widely used preprocessing tools generating NWB files have been developed, extensible frameworks for scientific analysis downstream of the NWB ecosystem are still under-represented. We present CICADA, a Python framework dedicated to analysis of neurophysiological data in the standardized NWB format. The toolbox is built as three hierarchically-organized packages: cicada-nwb (NWB access layer), cicada-analysis (plugin-based analysis engine and tool library), and cicada-gui (PyQt5 desktop application at the head of the pipeline). Beyond this architectural separation, CICADA is built around a central design principle: supporting a continuum from turnkey use to full modularity. Researchers can use the complete GUI-driven cicada-gui workflow without writing code, programmatically use existing analysis plugins from cicada-analysis, contribute to new analysis plugins, reuse utilities from cicada-tools, or build entirely custom pipelines on top of the cicada-nwb access layer alone. The same analysis plugin runs identically in interactive GUI and parameter-configured headless modes, enabling reproducible multi-session, multi-animal group analyses. We illustrate the versatility of CICADA with example analyses of behavioral, calcium imaging (two-photon and widefield) and extracellular electrophysiology datasets from rodent laboratories. CICADA is open source, actively maintained, and designed so that any laboratory can contribute at any level of the stack without modifying the core framework.

One of the prominent methods in neuroimaging data processing is SSM-PCA, which is based on principal component analysis and allows for the identification of diagnostically significant patterns in the form of statistical maps. We developed software, PIE Toolbox, employs SSM-PCA and classification based on the obtained diagnostic patterns revealed from functional and structural tomographic brain imaging. The program supports the entire analysis pipeline including preprocessing of brain images, diagnostic patterns extraction, building classification models, and prediction based on them. The resulting diagnostic patterns are weighted principal components obtained through SSM-PCA, or their linear combinations. PIE Toolbox allows selection of relevant structural and functional brain patterns, computation of their expression values in regions of interest, classification using support vector machines, and evaluation of model performance via cross-validation. This approach enables the use of patterns as features of intergroup differences for individual diagnosis. The software has been validated on both simulated and ADNI datasets.

We present a free and open-source, semi-automated, topologically robust pipeline for fitting cable models to 3D surface mesh morphology data of neuronal membranes, particularly suited to structures with complex shapes and topological holes. The motivation for this work is the discovery of morphologically complex neural spines on the auditory space-specific neurons of the barn owl (Tyto alba, Tyto furcata), dubbed "toric spines", notable for their high curvature, branching density, and holes/loops. Multicompartmental simulation software requires morphology to be represented as cable models (e.g., SWC format), yet existing software tools for fitting cable models to complex 3D surface meshes have not produced satisfactory results for toric spines, and loops are generally unsupported. We present the Mesh and Skeleton Cable Fitting (MASCAF) pipeline and software, which fits a cable model (e.g., SWC format) to a surface mesh using mean-curvature flow skeletonization. In this paper, we demonstrate how MASCAF is applied to fit cable models, how loops can be reconstructed in simulations with the Arbor and NEURON simulation software, and how the results can be validated using geometry and simulator-based methods. While non-tree morphologies such as toric spines are neuroanatomically special, our software pipeline provides a cable-model fitting approach for surface mesh data that is topologically robust, deterministic, open-source, and applicable to general morphologies, thereby closing a crucial gap between neuronal imaging and high-resolution simulation.

Connectomic reconstruction from large image volumes produces segmentation and synaptic-assignment errors that must be resolved to support downstream analyses. As datasets have grown larger and teams more distributed, proofreading has become a critical operational bottleneck. Workflows for proofreading and error correction have not scaled commensurately with connectomic data production and may not accommodate heterogeneous proofreader expertise and machine-generated candidate edits. New tools are therefore needed to organize, prioritize, and coordinate proofreading at volume scale. Here we present NeuVue, a task-management and prioritization framework that operationalizes proofreading through atomic, auditable tasks for individual and team review, multistage routing across proofreader cohorts, performance and volume-state tracking, and integration with community annotation, visualization, and analysis services. We report the use of NeuVue across two volumetric datasets, supporting scalable proofreading by over forty proofreaders and producing over fifty thousand edits. NeuVue provides a reproducible human-in-the-loop framework for generating, validating, and maintaining large connectomic datasets.

Three-dimensional (3D) whole-organ imaging and analysis at cellular resolution (termed 3D histology) provide profound insights into the organization and interactions of cells throughout organs. However, the quantitative analysis of these massive datasets remains a significant bottleneck due to the lack of integrated, user-friendly tools. Here, we present 3DBrainOne, an end-to-end ImageJ plugin that streamlines the essential 3D histological analysis of the mouse brain--from raw image preprocessing to region-wise quantification--within a single platform. 3DBrainOne features a robust whole-brain cell-counting module that uses a Difference-of-Gaussians (DoG) blob detection algorithm followed by a ResNet18-based deep learning classifier, enabling high-fidelity automatic whole-brain cell counting with a graphical user interface (GUI) for visual inspection and manual curation of analysis results. 3DBrainOne also supports multi-channel colocalization analysis. Furthermore, this platform includes modules for atlas alignment and brain-region-wise volumetric quantification, enabling brain region-resolved cell counting and structural analyses. As an ImageJ plugin, 3DBrainOne is compatible with a range of operating systems and hardware. In summary, 3DBrainOne is an integrated, versatile, and easy-to-use platform that will facilitate 3D histological analyses in experimental neuroscience.

Understanding vascular contributions to disease is a major unmet need. White matter lesions (WML) are an accepted imaging marker of cerebral small vessel disease, giving insights into its related pathologies. A unified approach for WML analyses in large multi-site data is lacking despite the need for pooling of data to overcome the limitations of often small heterogenous MRI studies which make subtyping and identifying patterns within disease groups difficult. Our ENIGMA-PD-WML pipeline is an open-source containerized pipeline containing all the code and packages required for pre-processing, processing and post-processing of T1-weighted and FLAIR data, outputting accurate and reproducible binary WML maps using a UNet approach. The pipeline provides a standardized image analysis approach for WML and outputs data in both native and MNI space to allow for sharing and pooling of data from multiple sites for large-data analysis. In addition to a reliable standardized approach for WML segmentation, key priorities when developing the pipeline included: usability, i.e., requiring minimal manual input and technical expertise to use, and suitability to run on various MRI scanners and acquisition parameters as is common in multi-site data. This paper describes the pipeline in detail, with rationale for each step, providing transparency and facilitating its usage to overcome reproducibility issues in large-scale WML analyses.

CT perfusion (CTP) is central to acute-stroke and oncologic imaging, yet quantitative outputs vary substantially across vendor software, undermining reproducibility. We present an open, transparent core (ctp-core) that fits first-pass time-attenuation curves with a gamma-variate model, derives perfusion indices (peak enhancement, time-to-peak, bolus-arrival time, and area under the curve) analytically from the fitted parameters, and renders parametric maps with the ASIST-Japan standardized lookup table (a-LUT) so that visualization is comparable across sites. Every parameter, bound, and processing step is exposed. The method is validated on Monte-Carlo synthetic curves with known ground truth; no confidential or patient data are used. Across signal-to-noise ratio (SNR) levels 5 to 100 (200 independent runs per level) the pipeline recovers peak time to within 0.03-0.52 s and peak amplitude to within 0.4-8.1% (mean absolute error), degrading monotonically with noise; at a representative SNR of 20 it recovers peak time within 0.13 s, peak amplitude within 2.0%, and bolus-arrival time within 0.51 s, with fit quality R-squared = 0.98. The reproducibility demonstration is deterministic (fixed seed) and re-runs to bit-stable metrics. All code, the synthetic-data generator, the standardized-visualization module, evaluation scripts, and a 34-test suite are released openly for independent verification. The contribution is a fully open, parameter-transparent gamma-variate plus standardized-visualization pipeline with reproducible synthetic benchmarks: a reference others can audit, reuse, and build on.

Molecular neuroimaging with positron emission tomography (PET) and single-photon emission computed tomography (SPECT) enables quantification of specific molecular targets in the living brain. Despite its scientific impact, molecular neuroimaging research has historically faced challenges due to high costs, small sample sizes, laboratory-specific analysis pipelines, and limited large-scale data sharing. These factors have hindered reproducibility and the broader reuse of valuable PET datasets. The OpenNeuroPET initiative was established to address these barriers by developing standards, infrastructure, and open-source tools for organizing, sharing, and analyzing molecular neuroimaging data. Through collaborations across Europe and North America, OpenNeuroPET has supported the PET extension of the Brain Imaging Data Structure (PET-BIDS), providing a standardized framework for PET datasets and metadata. Building on PET-BIDS, tools such as PET2BIDS, ezBIDS, and BIDSCoin facilitate data conversion and curation. In parallel, OpenNeuro now hosts PET-BIDS datasets for open sharing, while complementary platforms such as PublicnEUro enable GDPR-compliant controlled access. Emerging open-source workflows and BIDS applications further support automated, reproducible PET preprocessing and quantitative analysis, promoting harmonized processing across centers. Together, these developments mark an important step toward an open molecular neuroimaging ecosystem in which datasets, software, and workflows can be transparently shared, reused, and scaled for collaborative research.

AO_SCPLOWBSTRACTC_SCPLOWThe integration of electrophysiological recordings with multimodal neuroimaging data holds great promise for advancing our understanding of brain function and neurological disorders. To facilitate this endeavour, we present electro-MICA, an open-access Python toolbox designed to project electrophysiological features from scalp and intracranial electroencephalography (EEG) onto cortical and hippocampal surfaces generated by validated multimodal imaging ecosystems. The toolbox comprises two pipelines: one for intracranial EEG (iEEG) recorded with stereo-EEG depth electrodes, and one for scalp EEG source localization. Both pipelines are grounded in numerical solutions to the electromagnetic equations governing electric activity in the brain, solved using the Boundary Element Method. A key methodological contribution is the use of a current density double layer model for neural generators, which avoids the mathematical singularities introduced by conventional dipole-based models when electrodes are near the cortical surface, a situation that can arise in iEEG. Electrode contacts are additionally modeled with non-zero length, improving physical realism. Scalp EEG source localization is performed using eLORETA on a subject-specific three-layer head model derived from the anatomical input. Validation against empirical gamma-band iEEG data from 32 subjects demonstrates that the distributed generator model outperforms both distance-based and dipole-based alternatives. An illustrative clinical example demonstrates the toolboxs capacity to reveal associations between intracranial spike rates, cortical thickness, and anatomical connectivity in an epilepsy patient. Electro-MICA requires no parameter selection from the user, facilitating straightforward multimodal analyses in both research and clinical settings. The toolbox is available at github.com/MICA-MNI/electromica with extensive online documentation at electromica.readthedocs.io.

We now exist in the era of massive datasets from genomics, large language models, and all the known knowledge of humanity right at our fingertips. Much of this data is becoming more accessible; however, processing such data remains an ongoing issue across systems including high performance computing (HPC) infrastructures. Massively parallel computing (MPP) has solved this using a divide and conquer approach by splitting workloads across independent nodes (i.e., central processing units (CPU) allowing for higher scaling of data). The main engine for this in python is Ray; however, it has many issues including a large code space, security issues, debugging opacity, and memory management issues. Here, we present HydraMPP, a lightweight, ease of use and utilization, with high auditability, and with SLURM ergonomics.

BackgroundMagnetoencephalography (MEG) is a unique technique in human neuroimaging combining high temporal resolution (millisecond or faster) with moderate spatial resolution (several millimeter). While many software packages for MEG data analysis exist, there is no pipeline developed for the specific purpose of enabling the automated analysis of very large, multi-site datasets. ResultsThe ENIGMA consortium was developed to enable large scale collaborations in the fields of neuroimaging and genetics. To facilitate ENIGMA MEG working group data analysis, we developed the ENIGMA MEG pipeline. The first ENIGMA MEG working group project involves spectral analysis of resting state MEG data, thus our current pipeline is designed to carry out that task. The goals of the ENIGMA MEG pipeline include ease of use, automated processing wherever possible, detailed logging and quality assurance (QA) features, the use of the brain imaging data structure (BIDS) format, anonymized output, and consistent processing across vendors. The pipeline is built using the MNE-Python framework and incorporates a re-trained version of the MEGnet deep neural network algorithm for automated artifact detection. QA tools are designed to enable high throughput evaluation of a large number of subject datasets. All software is open source and available on GitHub (https://github.com/nih-megcore/enigma_MEG). We used our pipeline to process data from three publicly available MEG cohorts, demonstrating its functionality and compatibility with large-scale processing. ConclusionsWhile the current ENIGMA pipeline is limited to resting state data and spectral analysis for the current working group project, the software is highly modularized, allowing straightforward extension to other analysis questions. Further development of the tool to enable connectivity and task-based MEG analysis are planned. The ENIGMA MEG pipeline represents an important first step to augment the existing arsenal of analysis tools, enabling multi-site, high throughput data analysis.

The human cerebellum plays a central role in motor, emotional, and cognitive functions, and is implicated in many brain disorders. To improve the analysis of functional and anatomical imaging from the cerebellum, we introduce SUITPy, an improved and fully revised Python implementation of the widely used SUIT toolbox. For this new version, we developed a U-Net based model to automatically isolate the cerebellum from adjacent cortical tissue, which achieves higher fidelity than existing algorithms. The isolation works robustly without manual corrections for imaging data across the lifespan. We show that isolation and subsequent normalization to a cerebellum-only template lead to a more precise alignment of cerebellar structures across participants compared to normalization using a whole-brain template. We also show the utility of the cerebellar mask to prevent contamination of cerebellar functional data from surrounding cortical structures. The toolbox also provides functionality for visualizing cerebellar data on a flatmap, along with a range of anatomical and functional cerebellar atlases, thereby offering an essential tool that enables accurate cerebellar analysis across the lifespan.

SignificanceAccurate and reproducible optode placement is crucial for obtaining high-quality fNIRS data in both individual and group-level neuroimaging studies. Conventional optode/probe montage design tools usually transform a probe layout defined in 2D Cartesian space onto a 3D head surface using a mass-spring model. Such mechanical transformation, combined with the indirect mapping between the 2D probe definition and the 3D target space, can introduce placement variations across different head surfaces and subjects. AimWe introduce NeuroCaptain v2, an open-source Blender-based add-on designed to enable interactive, anatomically guided optode design, registration, and cortical sensitivity visualization for fNIRS head-cap and probe creation. ApproachNeuroCaptain v2 enables researchers to add, move, and edit fNIRS sources and detectors directly over a 3D head surface mesh, defining anchored optode positions, as well as setting the stiffness of the springs between adjacent optodes. It then utilizes Blenders built-in physical simulation engine to relax the initial probe layout to satisfy the mechanical constraints. With the built-in mesh-based Monte Carlo (MMC) and diffusion-solver Redbird, NeuroCaptain v2 computes and renders 3D sensitivity maps to guide iterative optode adjustment. The resulting 3D optode layout is stored in the form of barycentric coordinates defined in a 10-20 landmark mesh, enabling consistent probe transfer across different head models. ResultsWe demonstrate interactive 3D montage design, cross-head-atlas probe registration, and cortical sensitivity visualization across multiple head geometries. Registering a probe across seven neurodevelopmental head atlases, the proposed anatomical-coordinate approach yields a mean per-optode standard deviation of 2.29 mm, a roughly 74% reduction in cross-subject placement variability compared to 8.68 mm using a conventional 2D-to-3D registration. ConclusionsNeuroCaptain v2 provides a reproducible, fully open-source workflow for fNIRS probe montage design that facilitates anatomically guided probe development and cross-subject registration directly in a three-dimensional anatomical environment.

Hippocampal area CA2 has recently emerged as a critical region for social recognition memory. Furthermore, this understudied region has been implicated in psychiatric diseases and neurodegenerative diseases. There has been accumulating evidence indicating that the pyramidal neurons (PNs) in area CA2 exhibit functional specializations that correlate with somatic position in stratum pyramidale (sp). In this study, we investigated the morphological differences in dendritic architecture of CA2 PNs with a focus on the radial gradient, i.e., along the deep-superficial axis of the sp. We conducted a comprehensive morphological analysis including Sholl intersection profiles, branching order distributions, root angle distributions, and dendritic cable lengths. We found that CA2 PNs have fewer oblique dendrites and a larger number of tuft-like dendrites as compared to CA1 PNs. Furthermore, within the CA2 population, we found that many of the dendritic structural features gradually changed along the radial axis from deep to superficial somatic location, indicating a continuum of dendritic morphology rather than two sharply defined subtypes of pyramidal neurons. This morphological characterization may serve as a starting point to better understand the corresponding functional organization of CA2. The gradual difference between deeper and superficial CA2 PNs suggests a continuum of their computational capabilities beyond two binary functional classes. In briefUsing several methods, we examine the dendritic morphology of over 130 CA2 and CA1 pyramidal neurons and find that many properties such as the cable length and terminal numbers of the dendritic arbors vary as a with the location of the soma in the pyramidal layer. HighlightsO_LIWe use scholl analysis, graph theory and machine learning techniques to quantify the different dendritic morphologies of CA2 pyramidal neurons. C_LIO_LIMany properties of CA2 pyramidal neuron apical dendrites vary as a function of somatic location in the pyramidal layer. C_LIO_LIMore superficial CA2 pyramidal neurons have longer oblique apical dendrites, and shorter tuft dendrites. C_LI

Background and ObjectiveNormative modeling is a key tool for understanding brain alterations in neurodegenerative diseases, such as cerebellar-type multiple system atrophy. However, existing methods lack interpretability and fail to capture clinically meaningful pathological changes. This study presents DINMC, a Deep Interpretable Normative Model Construction framework, which combines autoencoder-based learning with statistical hypothesis testing to better capture and interpret disease-specific neu-roanatomical changes. MethodsThe DINMC framework constructs normative models using neuroimaging data from multi-site large healthy cohorts. It utilizes a U-shaped convolutional autoencoder to train these models, which are then applied to reconstruct brain features from both patients and healthy controls within the same study cohort. Pathological confidence values are derived by fusing original and deviation feature spaces, offering a measure of disease-related pathology reflected in each dimension of the features. The framework was validated through statistical analysis and prognostic classification and regression tasks. ResultsThe pathological confidence provides valuable insights into the neuroanatomical regions most affected by the disease, as well as the correlation between changes in these regions and clinical assessment scales. Our optimal model outperform traditional methods in prognostic prediction tasks, with an AUC of 0.972 for classification tasks and an R2 of 0.432 for regression tasks. ConclusionDINMC provides a novel and interpretable framework for neuroimaging analysis. By combining deep learning and statistical hypothesis testing, this framework offers a unique solution to improving both the interpretability and performance of normative models in neuroimaging. The approach is scalable to other neuroimaging datasets, offering a versatile tool for broader biomedical applications.

Despite growing understanding of the benefits of having Findable, Accessible, Interoperable, and Reusable (FAIR) data, many datasets still cannot be shared. Federated analysis methods can enable multisite studies that do not require the sharing of participant-level information. However, there are many practical hurdles that prevent the large-scale adoption of federated methods. We discuss challenges related to cross-site data preparation for federated learning, present solutions offered by recent neuroinformatics projects, and showcase an example of tool integration applied to neurodegenerative disease data.

Currently, there is no consensus about how investigators should format their NIBS data for sharing. This presents a barrier to the advancement of big data analyses because it requires time-consuming operations to generate consistent formats across different shared datasets. Recently, we launched Big non-invasive brain stimulation data (Big NIBS data), an open-access platform and repository for NIBS data (https://www.bignibsdata.com/), providing a structured mechanism for researchers to share NIBS data. However, the reusability and interoperability of data uploaded to Big NIBS data is restricted by the absence of a common data structure. The current paper addresses this problem by creating the NIBS data analysis structure (NIBS-DAS), a template pipeline for the layout, management, and analysis of collated NIBS outcome data. While its primary purpose is to provide a template layout for uploading collated data to the Big NIBS data repository, NIBS-DAS also offers guidelines for the management and analysis of collated NIBS data, thereby forming a data analysis pipeline that can be freely used by the NIBS field in general. We anticipate that NIBS-DAS will serve to facilitate data sharing on the Big NIBS data platform and promote greater standardisation of data management and analytical practices in the NIBS field.

BackgroundThe relevance of spontaneous activity has been unlocked thanks to recent large scale recordings that revealed, via Shared Variance Component Analysis (SVCA), the high-dimensional nature of the ongoing activity. A fundamental problem is how the dimension modifies when more neurons are included in the analysis. Contradictory results have been reported on this subject based on SVCA and Principal Component Analysis (PCA). New MethodWe investigate pro et contra of SVCA and PCA for the identification of reliable responses encoding underlying state variables. We focus on common features of the spectra of the reliable variances (RVs) and on their dimensionality. The analysis is demonstrated on previously published Ca2+ data from the visual and the dorsal cortex in head fixed mice during spontaneous behavior. ResultsRVs grow proportionally to the number N of neurons and show a power-law decay k- with the k-th SVC dimension over a range bounded by a maximal dimension kc, initially diverging as N 1/ and then saturating at sufficiently large N. The reliable dimensionality, estimated with different methodologies, also shows a clear saturation to an asymptotic value for large N. Furthermore, its value decreases when becomes larger, as demonstrated by employing experimental data as well as theoretical predictions. ConclusionWe have shown that SVCA is an extremely effective tool to extract reliable features from the neural signals, and that the exponent represents a biomarker able to reveal the level of correlation of the neurons as well as the dimensionality of the reliable space. HighlightsO_LIAdvantages and drawbacks of Shared Variance Component Analysis to extract reliable signals from neural data C_LIO_LIComparison of different methods to estimate reliable neural dimensionality associated to spontaneous activity C_LIO_LIAnalytical expressions of embedding dimensionality for power-law decaying reliable variances C_LIO_LIBounded growth of the dimensionality with the number of neurons C_LI

Traumatic brain injury produces widespread axonal damage can be assessed histologically using amyloid precursor protein (APP) immunohistochemistry, which labels injured axonal profiles at cellular resolution [1, 2]. However, quantification of APP pathology remains a major bottleneck: annotation is manual, time-consuming, spatially localized, and variable across raters, limiting scalability and reproducibility. This limitation is particularly important in studies that use histology as a reference for neuroimaging or other tissue-level measurements, where cellular APP pathology must be quantified in a spatial form that can be aligned with imaging abnormalities. Here, we introduce PIGMENT, an annotation-efficient deep-learning framework for automated segmentation and quantification of APP-positive pathology in porcine white matter histology. PIGMENT uses a compact SegFormer-B0 architecture trained on 525 expert-annotated 512 x 512-pixel tiles from four APP-stained sections across three pigs. Because APP-positive profiles are sparse, fragmented, stain-variable, and morphologically diverse, PIGMENT combines limited expert labels with APP-specific augmentation designed to model variation in APP-positive intensity, size, continuity, fragmentation, and local tissue context. We evaluated PIGMENT using an instance-level detection rate that measures whether discrete APP-positive components are localized. Across held-out APP-stained data, PIGMENT achieved a mean instance-level detection rate of 0.86. Across the configurations tested, the highest mean detection rate was achieved by a training set that included sections from different animals, suggesting that annotation diversity may be an important factor under limited-label conditions. By extending limited high-confidence expert annotations into whole-section APP burden maps, PIGMENT provides a scalable framework for characterizing the extent and spatial distribution of traumatic axonal injury. These maps may support future studies that align histological injury burden with imaging-derived measures.

Equilibrium propagation (EP) is a biologically plausible alternative to backpropagation that has demonstrated competitive performance across a range of machine learning tasks. Recent work has extended EP to spiking neural networks (SNNs), leveraging leaky integrate-and-fire (LIF) neurons and spike-based plasticity rules to improve biological realism while maintaining strong performance. In this work, we propose an EP-based SNN framework that combines LIF neural dynamics with a predictive learning rule, replacing conventional spike-timing-dependent plasticity (STDP) with a learning rule more directly aligned with predictive coding principles. We evaluate the proposed model on multiple image classification benchmarks, including MNIST, KMNIST, and Fashion-MNIST, and compare its performance with a BP-trained LIF SNN baseline. Our results show that the proposed EP-based LIF model (EP+LIF) achieves competitive accuracy across datasets, with performance approaching that of the BP-trained counterpart (BP+LIF) while relying on a biologically motivated local learning rule. In addition, analysis of hidden-layer spiking activity reveals that EP+LIF produces more persistent hidden-state activity, whereas BP+LIF yields sparser spiking representations. These results demonstrate that predictive learning can support effective EP-based training in LIF spiking networks, while also highlighting differences in activity patterns that motivate future work on activity regulation and sparse spiking dynamics.