Biology subjects

Vanduffel, W.

Publications and source records attributed to Vanduffel, W..

15 recordsLinked to original sources

bioRxiv2026

Topographic and somatotopic organization of functional connectivity between the intraparietal sulcus and primary somatosensory cortex in macaque monkeys

The posterior parietal cortex integrates somatosensory information with signals supporting action, spatial cognition, and multisensory processing, yet the fine-scale topographic relationship between the intraparietal sulcus (IPS) and primary somatosensory cortex (S1) remains poorly understood. Here, we used resting-state fMRI in 10 awake rhesus macaques to characterize functional connectivity between four S1 subregions (areas 3a, 3b, 1, and 2) and 223 single-voxel seeds densely sampling an IPS-centered parietal territory. Across S1 subregions and hemispheres, IPS-S1 connectivity exhibited a highly structured spatial organization characterized by systematic anteroposterior and mediolateral gradients and a prominent semi-oval topology following the geometry of the intraparietal sulcus. Connectivity was generally stronger toward the cortical banks and convexities and weaker near the sulcal fundus, a pattern that could not be explained by reduced local temporal signal-to-noise ratio. Unsupervised hierarchical clustering independently recovered this spatial organization and identified connectivity-defined subdivisions that only partially corresponded to classical cytoarchitectonic boundaries. Along the S1 mediolateral axis, prominent troughs in cluster-averaged connectivity profiles corresponded to several previously described somatotopic transitions, allowing to consistently map putative boundaries between tongue and face representations and between hand and trunk-leg representations. Based on these boundaries, individual IPS clusters exhibited connectivity with multiple S1 body-part sectors, with the pattern of connectivity across these sectors varying across IPS clusters and S1 subregions. Together, our findings reveal that IPS-S1 functional connectivity is organized by a large-scale sulcal topology while preserving fine-grained features of S1 somatotopic organization. These findings suggest that the functional organization of the IPS is shaped by multiple spatial dimensions, including large-scale sulcal topology and the organization of S1 subregions and body-part representations, which may together contribute to the functional specialization of individual IPS regions.

neuroscience↗

bioRxiv2026

Probabilistic Retinotopic Parcellation of the Macaque Visual Cortex

Probabilistic brain atlases provide anatomically and functionally interpretable normative references that summarize population-level organization while explicitly representing spatial uncertainty. Yet such resources remain scarce due to the resource-intensive experimental efforts required to construct them. Here, we present a probabilistic retinotopic atlas of the macaque visual cortex, derived from contrast-enhanced phase-encoded fMRI data acquired in 13 subjects. The dataset includes a 50% probability parcellation covering 19 visual areas, individual subject labels, and voxel-wise probability maps for each area, all registered to the MEBRAINS macaque template. By combining a consensus parcellation with spatial estimates of confidence for each visual area, this atlas enables more informed anatomical localization and interpretation than deterministic or single-subject-based atlases. As a standardized reference for the macaque visual cortex, it supports experimental design, data interpretation, and multimodal data integration while providing a quantitative framework for investigating the developmental and evolutionary principles that shape the primate visual cortex.

neuroscience↗

bioRxiv2026

Hyperalignment Reveals Shared Information in Macaques' Idiosyncratic Fine-Grained Movie fMRI Patterns

Response hyperalignment (RHA) of fMRI patterns acquired during movie-viewing in 12 rhesus monkeys revealed shared representational spaces despite idiosyncratic functional topographies. RHA greatly improved inter-subject correlation of movie response time-series in occipital, temporal, and prefrontal cortices and afforded highly accurate between-subject decoding of movie time-points and estimation of idiosyncratic functional topographies. These results demonstrate that nonhuman primates share high-dimensional, high-capacity representational spaces encoded in idiosyncratic fine-grained functional topographies.

neuroscience↗

bioRxiv2026

MacaSurfer: unified surface-volume mapping of the macaque brain across the lifespan

Macaque brain MRI is central to translational and comparative neuroscience, yet multi-site, longitudinal, and cross-species analyses are hindered by a lack of unified, automated structural processing tools. Existing pipelines, mostly adapted from human neuroimaging or restricted to fragmented steps, fail to provide robust surface-volume representations across heterogeneous acquisitions and developmental stages. Here we introduce MacaSurfer, a fully automated, containerized framework for unified surface-volume mapping of the macaque brain across the lifespan. MacaSurfer features components tailored for macaque anatomy: a tissue segmentation model, a tissue-guided bias-field correction method optimizing structural mapping from T1-weighted images alone, topology-aware surface reconstruction, and surface-aware volumetric registration. Validated on 1,346 imaging sessions from 965 macaques across 39 international sites (spanning 2 weeks to 23 years of age), MacaSurfer demonstrated exceptional anatomical consistency, test-retest precision, and robustness against image degradation. Leveraging MacaSurfer-derived morphometry, we established normative trajectories from 835 macaques, providing a standardized reference for downstream individualized deviation analysis. MacaSurfer is openly available with source code, containers, and pretrained models, offering a reproducible ecosystem to accelerate developmental, translational, and comparative neuroimaging.

neuroscience↗

bioRxiv2026

Volumetric functional ultrasound imaging in macaques

Linking circuit level activity to large scale functional organization requires imaging methods combining high spatial resolution, broad coverage, and single trial sensitivity. We present volumetric functional ultrasound imaging (3D-fUS) in behaving macaques, enabling imaging of ~1 cm3 cortical volumes at high spatiotemporal resolution (100 x 150 x 150 m3 voxels, 1.67 Hz). Visually evoked responses were reliably detected at the level of single trials and single voxels, substantially reducing experimental time. To enable model-based analyses analogous to functional magnetic resonance imaging (fMRI), we estimated a canonical fUS hemodynamic response function (fUS-HRF) that was consistent across subjects, cortical areas, and visual stimuli and was well approximated by a gamma function. Compared with canonical fMRI HRFs, the fUS-HRF exhibited faster dynamics, enabling shorter and more closely spaced stimulus presentations. Together, these results establish 3D-fUS as a fast, volumetric, and circuit relevant imaging modality for efficient investigation of distributed cortical dynamics in primates.

neuroscience↗

bioRxiv2025

OfUSA: OpenfUS Analyzer, a versatile open-source framework for the analysis and visualization of functional ultrasound imaging data across animal models

Functional ultrasound (fUS) imaging is rapidly gaining interest for its unprecedented ability to study large-scale brain dynamics, yet its adoption and broader dissemination have been hindered by the lack of standardized tools and methodologies to analyze and interpret its rich datasets. We present OpenfUS Analyzer (OfUSA), a companion software suite designed to help researchers quickly engage with fUS data and perform the full range of analyses needed to generate publication-ready results and figures without relying on additional software. OfUSA offers a versatile and modular architecture including preprocessing, recording quality assessment, signal dynamics exploration, statistical analysis and visualization. These functions are separated yet easily combined into analytic pipelines through a programming-free graphical interface. The framework can be applied across species and experimental contexts, either by registering data to anatomical atlases, as shown here for the mouse brain, or by analyzing data without atlas constraints, as illustrated in a primate dataset. This flexibility, together with its comprehensive functionality, makes OfUSA a practical solution for standardized and reproducible analysis of fUS data in both preclinical and translational research. Using OfUSA, we demonstrate the capacity to detect stimulus-evoked responses with high sensitivity, identify their spatial localization within brain networks, and quantify both their extent and temporal dynamics. These results highlight the softwares ability to capture robust activation patterns and provide detailed insights into brain function, thereby accelerating the use of fUS as a powerful tool for systems neuroscience. HighlightsWe present OpenfUS Analyzer (OfUSA), a novel software platform for the complete analysis of functional ultrasound (fUS) datasets. OfUSA combines a user-friendly graphical interface with a standardized, flexible workflow and powerful visualization tools, making it an ideal solution for fUS researchers at all experience levels. The softwares utility is first demonstrated through the analysis of rodent fUS data using a standardized atlas, while its versatility is further emphasized by the successful analysis of a primate fUS dataset without a template, thereby illustrating its adaptability to non-standard experimental conditions.

neuroscience↗

bioRxiv2025

CoreTIA: a modular, statistically robust transduction inhibition assay for AAV neutralization

Adeno-associated virus (AAV) gene therapy is often limited by pre-existing neutralizing antibodies (NAbs), yet current assays for NAb detection lack standardization and rarely quantify uncertainty, complicating cross-study comparisons. We present coreTIA (core Transduction Inhibition Assay), a modular experimental protocol combined with a statistically robust analysis pipeline that delivers precise, reproducible NAb titers with quantified uncertainty for every result. coreTIAs statistical framework enables robust estimation of neutralization even when dilution series are incomplete, helping to reduce repeat testing and minimizing sample volume requirements. Evaluation and refinement of key assay parameters support consistent performance across AAV serotypes. By providing a protocol and analysis suite as an open resource, coreTIA facilitates more consistent and transparent NAb measurement, potentially aiding assay harmonization and regulatory assessment, addressing a key barrier to progress in gene therapy research and development.

immunology↗

bioRxiv2024

The macaque ventral intraparietal functional connectivity patterns reveal an anterio-posterior specialization mirroring that described in human ventral intraparietal area

The macaque monkeys ventral intraparietal area (VIP) in the intraparietal sulcus (IPS) responds to visual, vestibular, tactile and auditory signals and is involved in higher cognitive functions including the processing of peripersonal space. In humans, VIP appears to have expanded into three functionally distinct regions. Macaque VIP has been divided cytoarchitonically into medial and lateral parts; however, no functional specialization has so far been associated with this anatomical division. Functional MRI suggests a functional gradient along the anterior-posterior axis of the macaque IPS: anterior VIP shows visio-tactile properties and face preference, whereas posterior VIP responds to large-field visual dynamic stimuli. This functional distinction matches with functional differences among the three human VIP regions, suggesting that a regional specialization may also exist within macaque VIP. Here, we characterized the ipsilateral, whole-brain functional connectivity, assessed during awake resting state, along VIPs anterior-posterior axis by dividing VIP into three regions of interest (ROIs). The functional connectivity profiles of the three VIP ROIs resembled anatomical connectivity profiles obtained by chemical tracing. Anterior VIP was functionally connected to regions associated with motor, tactile, and proprioceptive processing and with regions involved in reaching, grasping, and processing peripersonal space. Posterior VIP had the strongest functional connectivity to regions involved in motion processing and eye movements. These profiles are consistent with the connectivity profiles of the anterior and posterior VIP areas identified in humans. Viewed together, resting state functional connectivity, task-related fMRI and anatomical tracing consistently suggest specific functional specializations of macaque anterior and posterior VIP. This specialization corroborates the distinction of VIP into three anatomically and functionally separate VIP areas in humans.

neuroscience↗

bioRxiv2024

Comparative Analysis of Human-Chimpanzee Divergence in Brain Connectivity and its Genetic Underpinnings

Chimpanzees (Pan troglodytes) are humans closest living relatives, making them the most directly relevant comparison point for understanding human brain evolution. Zeroing in on the differences in brain connectivity between humans and chimpanzees can provide key insights into the specific evolutionary changes that might have occured along the human lineage. However, conducting comparisons of brain connectivity between humans and chimpanzees remains challenging, as cross-species brain atlases established within the same framework are currently lacking. Without the availability of cross-species brain atlases, the region-wise connectivity patterns between humans and chimpanzees cannot be directly compared. To address this gap, we built the first Chimpanzee Brainnetome Atlas (ChimpBNA) by following a well-established connectivity-based parcellation framework. Leveraging this new resource, we found substantial divergence in connectivity patterns across most association cortices, notably in the lateral temporal and dorsolateral prefrontal cortex between the two species. Intriguingly, these patterns significantly deviate from the patterns of cortical expansion observed in humans compared to chimpanzees. Additionally, we identified regions displaying connectional asymmetries that differed between species, likely resulting from evolutionary divergence. Genes associated with these divergent connectivities were found to be enriched in cell types crucial for cortical projection circuits and synapse formation. These genes exhibited more pronounced differences in expression patterns in regions with higher connectivity divergence, suggesting a potential foundation for brain connectivity evolution. Therefore, our study not only provides a fine-scale brain atlas of chimpanzees but also highlights the connectivity divergence between humans and chimpanzees in a more rigorous and comparative manner and suggests potential genetic correlates for the observed divergence in brain connectivity patterns between the two species. This can help us better understand the origins and development of uniquely human cognitive capabilities.

neuroscience↗

bioRxiv2023

Multiple focal pulvinar projection fields in the macaque cortex

The pulvinar, the largest nucleus of the thalamus, is functionally heterogeneous and involved in multiple cognitive functions. It has been proposed to act as a functional hub of cortical processes due to its extensive reciprocal connectivity with the cortex. However, its role in cognition is not fully understood yet. Here, we posit that an improved understanding of its functional connectivity with the cortex is needed to better capture the cognitive functions of this nucleus. To address this question, we characterize the pulvino-cortical functional connectivity along the ventro-dorsal, antero-posterior and medio-lateral axes, using awake resting state data from ten adult macaques. We first report two global cortical functional connectivity gradients along the antero-posterior and ventro-dorsal pulvinar gradients, that match remarkably well the structural connectivity gradients described by anatomical approaches. In addition to these global gradients, multiple local cortical pulvinar projection fields can be identified at the sulci level such as in the lateral sulcus (LS), the intraparietal sulcus (IPS), the principal sulci (PS) and the anterior cingulate cortex (ACC). For most sulci, we show that functional pulvino-cortical projection fields follow the major anatomical axis of these different sulci (e.g. the ventro-dorsal axis for the LS and the antero-posterior axis for the IPS). Other sulci, such as the superior temporal sulcus, the posterior cingulate cortex or the central sulcus, display multiple projection fields from the pulvinar. Although substantial inter-individual differences exist, the general functional connectivity patterns are remarkably consistent across hemispheres and individuals. Overall, we propose that these multiple pulvinar projection fields correspond to a fundamental principle of pulvino-cortical connectivity and that a better understanding of this connectional organization will shed light on the function of pulvino-cortical interactions and the role of the pulvinar in cognition at large.

neuroscience↗

bioRxiv2023

MEBRAINS 1.0: a new population-based macaque atlas

Due to their fundamental relevance, the number of anatomical macaque brain templates is constantly growing. Novel templates aim to alleviate limitations of previously published atlases and offer the foundation to integrate multiscale multimodal data. Typical limitations of existing templates include their reliance on one subject, their unimodality (usually only T1 or histological images), or lack of anatomical details. The MEBRAINS template overcomes these limitations by using a combination of T1 and T2 images, from the same 10 animals (Macaca mulatta), which are averaged by the multi-brain toolbox for diffeomorphic registration and segmentation. The resulting volumetric T1 and T2 templates are supplemented with high quality white and gray matter surfaces built with FreeSurfer. Human-curated segmentations of pial surface, white/gray matter interface and major subcortical nuclei were used to analyse the relative quality of the MEBRAINS template. Recently published 3D maps of the macaque inferior parietal lobe and (pre)motor cortex were warped to the MEBRAINS surface template, thus populating it with a parcellation scheme based on cyto- and receptor architectonic analyses. Finally, 9 CT scans of the same monkeys were registered to the T1 modality and co-registered to the template. Through its main features (multi-subject, multi-modal, volume-and-surface, traditional and deep learning-based segmentations), MEBRAINS aims to improve integration of multi-modal multi-scale macaque data and is quantitatively equal or better compared to currently widely used macaque templates. The template is integrated in the EBRAINS and Scalable Brain Atlas web-based infrastructures, each of which comes with its own suite of spatial registration tools.

neuroscience↗

bioRxiv2023

Brain mechanisms of reversible symbolic reference:a potential singularity of the human brain

The emergence of symbolic thinking has been proposed as a dominant cognitive criterion to distinguish humans from other primates during hominization. Although the proper definition of a symbol has been the subject of much debate, one of its simplest features is bidirectional attachment: the content is accessible from the symbol, and vice versa. Behavioural observations scattered over the past four decades suggest that this criterion might not be met in non-human primates, as they fail to generalise an association learned in one temporal order (A to B) to the reverse order (B to A). Here, we designed an implicit fMRI test to investigate the neural mechanisms of arbitrary audio-visual and visual-visual pairing in monkeys and humans and probe their spontaneous reversibility. After learning a unidirectional association, humans showed surprise signals when this learned association was violated. Crucially, this effect occurred spontaneously in both learned and reversed directions, within an extended network of high-level brain areas, including, but also going beyond, the language network. In monkeys, by contrast, violations of association effects occurred solely in the learned direction and were largely confined to sensory areas. We propose that a human-specific brain network may have evolved the capacity for reversible symbolic reference.

neuroscience↗

bioRxiv2020

Face neurons in human visual cortex

The exquisite capacity of primates to detect and recognize faces is crucial for social interactions. Although disentangling the neural basis of human face recognition remains a key goal in neuroscience, direct evidence at the single-neuron level is virtually nonexistent. We recorded from face-selective neurons in human visual cortex, in a region characterized by functional magnetic resonance imaging (fMRI) activations for faces compared to objects (i.e. the occipital face area, OFA). The majority of visually responsive neurons in this fMRI activation showed strong selectivity at short latencies for faces compared to objects. Feature scrambled faces and face-like objects could also drive these neurons, suggesting that the OFA is not tightly-tuned to the visual attributes that typically define whole human faces. These single-cell recordings within the human face processing system provide vital experimental evidence linking previous imaging studies in humans and invasive studies in animal models.

neuroscience↗

bioRxiv2020

Direct comparison of population receptive fields from fMRI and large-scale neurophysiological recordings in awake non-human primates.

Population receptive field (pRF) modeling is a popular fMRI method to map the retinotopic organization of the human brain. While fMRI-based pRF-maps are qualitatively similar to invasively recorded single-cell receptive fields in animals, it remains unclear what neuronal signal they represent. We addressed this question in awake non-human primates comparing whole-brain fMRI and large-scale neurophysiological recordings in areas V1 and V4 of the visual cortex. We examined the fits of several pRF-models based on the fMRI BOLD-signal, multi-unit spiking activity (MUA) and local field potential (LFP) power in different frequency bands. We found that pRFs derived from BOLD-fMRI were most similar to MUA-pRFs in V1 and V4, while pRFs based on LFP gamma power also gave a good approximation. FMRI-based pRFs thus reliably reflect neuronal receptive field properties in the primate brain. In addition to our results in V1 and V4, the whole-brain fMRI measurements revealed retinotopic tuning in many other cortical and subcortical areas with a consistent increase in pRF-size with increasing eccentricity, as well as a retinotopically specific deactivation of default-mode network nodes similar to previous observations in humans.

neuroscience↗

bioRxiv2018

A new view of dorsal visual cortex in macaques revealed by submillimeter fMRI

Macaque dorsal occipital cortex is generally thought to contain one elongated third-tier area, V3d, extending along most of the rostral V2d border. In contrast, our submillimeter retinotopic fMRI maps (0.6 mm isotropic voxels, achieved by implanted phased-array receive coils) consistently show three sectors anterior to V2d. The dorsal (mirror-image) sector complies with the traditional V3d definition, and the middle (non-mirror image) sector with V3A. The ventral (mirror-image) sector bends away from V2d, as does VLP in marmosets and DLP in owl monkeys, and represents the entire contralateral hemifield like V3A. Its population receptive field size, however, suggests that this ventral sector is another fourth-tier area caudal to V4d. Hence, contrary to prevailing views, the retinotopic organization of cortex rostral to V2d differs substantially from widely accepted models. Instead, it is evolutionarily largely conserved in Old and New World monkeys.

neuroscience↗