Biology subjects

Arcaro, M. J.

Publications and source records attributed to Arcaro, M. J..

10 recordsLinked to original sources

bioRxiv2026

Brainana: an end-to-end preprocessing framework for macaque neuroimaging

Macaque MRI bridges non-invasive systems neuroscience with cellular and circuit-level mechanisms, but preprocessing tools remain difficult to integrate and deploy reproducibly. We present Brainana, an automated, BIDS-compatible preprocessing and visualization framework for macaque neuroimaging. Brainana integrates structural and functional preprocessing, cortical surface reconstruction, quality control, transform tracking, and atlas projection within a containerized package, with cloud access for users without local compute. Macaque-trained deep learning models support brain extraction and tissue segmentation, while image orientation standardization and macaque-specific surface reconstruction optimizations address variability across acquisitions. A viewer automatically organizes derivatives and links volumetric and surface data, enabling users to inspect anatomy, cortical measures, atlas delineations, and activity maps without neuroimaging expertise. Across 23 imaging sites, Brainana processed heterogeneous data from 130 monkeys, yielding anatomical correspondence, reliable native-space surfaces, localized task-evoked activations, and reproducible brain-wide resting-state correlations. Brainana enables reproducible, scalable, and accessible macaque MRI analysis, cross-study comparison, and multimodal integration.

neuroscience↗

bioRxiv2026

Transformation-tolerant object recognition in tree shrews despite lacking a fovea

Object recognition depends on the ability to extract stable representations across changes in how they are viewed, yet it remains unclear how this capacity depends on visual acuity and cortical hierarchy. We combined behavioral testing and computational modeling to determine whether tree shrews, close relatives of primates with lower spatial acuity, can perform transformation-tolerant object recognition. Front-end modeling incorporating species-specific optics and photoreceptor sampling showed that, when scaled for acuity, tree shrew retinal filtering preserves the similarity structure of natural image categories relevant for object recognition. Behaviorally, tree shrews reliably discriminated complex objects across variations in position, scale, and viewpoint, including when embedded within natural scenes, and generalized to novel exemplars. Their recognition behavior was best explained by visual features emphasizing differences in global shape and size between objects and by representations from intermediate and deep layers of hierarchical neural network models. These results demonstrate that visual processing supporting object-level generalization can arise within visual systems lacking high-acuity front-end optics and establish the tree shrew as a key model for understanding the computational and evolutionary origins of high-level vision.

animal behavior and cognition↗

bioRxiv2026

Geometric constraints in the development of primate extrastriate visual cortex

Sensory systems are organized into topographic maps that shape information flow and computation across cortical circuits. Although the mechanisms establishing primary sensory maps are well characterized, how higher-order maps emerge across neocortex is unclear. Because the probability and strength of cortical connections fall off steeply with distance along a folded surface, the geometry of the cortex may be a major factor shaping the organization of higher-order maps. To test this in a well-characterized sensory system, we develop a growth model embedded in the folded surface geometry of the macaque visual cortex, using fMRI-defined V1 retinotopy as the sole functional anchor. Cortical organization emerges through algorithmic growth from primary visual cortex, governed by distance-dependent activity correlations and competition among developing projections. Without imposing areal boundaries, map orientations, or predefined topographic layouts, this process generates multiple retinotopic maps with systematic mirror reversals and smooth gradients that reflect key structural features of fMRI-derived extrastriate maps. Parameters estimated on a population template generalize across individual macaques, while individual cortical geometry accounts for fine-scale map variation around a common retinotopic scaffold. These results suggest that conserved growth rules acting on folded cortical surfaces produce stereotyped higher-order retinotopic organization under minimal explicit specification.

neuroscience↗

bioRxiv2025

Metabolic organization of macaque visual cortex reflects retinotopic eccentricity and category selectivity

Neural activity requires energy metabolism, and the brains metabolic architecture varies across regions. Yet, it remains unclear whether these variations are meaningfully related to the functional and perceptual demands of cortical processing. In high-level visual cortex, category-selective regions, such as those preferentially responding to faces and scenes, are consistently distributed along a topographic axis that varies in sensitivity to spatial scale, a feature dimension that imposes differing metabolic demands at the level of the retina. This axis reflects a broader organizing principle of the visual system: retinotopic eccentricity, the topographic mapping of visual space relative to gaze. Here, we tested whether cortical metabolic architecture reflects this principle by aligning in vivo fMRI maps of eccentricity and visual category selectivity with ex vivo cytochrome oxidase (CO) histology, a marker of oxidative metabolism, in macaque visual cortex. We found that face-selective region ML, which is biased toward central vision, exhibits higher CO intensity than the peripherally-biased scene-selective region LPP. More broadly, CO intensity covaries with eccentricity across the entire occipitotemporal cortex, though this gradient only partially accounts for the elevated CO in ML. These findings reveal a close correspondence between cortical energy consumption and retinotopic representation, suggesting that metabolic resources are shaped by the processing demands of visual perception.

neuroscience↗

bioRxiv2025

Hierarchical Processing of Natural Scenes in the Human Pulvinar

The hierarchical organization of the ventral visual cortex has been the focus of theories and computational models characterizing high-level visual processing and object recognition, often overlooking potential contributions of subcortical structures. The pulvinar, through its extensive reciprocal connections with ventral visual cortex, is well-positioned to play a prominent role in high-level visual recognition processes. Here, we investigated whether the pulvinar plays such a role using a high-resolution 7T fMRI dataset of responses to tens of thousands of natural scenes. Encoding models testing the representation of different stimulus features revealed a pulvinar region selective for bodies and faces presented within the contralateral visual hemifield. Model-free analyses demonstrated that this region is predominantly co-active with body- and face-selective cortical areas during natural scene viewing. This functional specificity was embedded within a broader gradient of cortical correlations across the pulvinar mirroring the hierarchical organization of ventral visual cortex. These findings challenge cortico-centric models of object vision and implicate a role of the pulvinar in high-level vision. More broadly, these results demonstrate that principles of cortical organization, including functional clustering and hierarchical organization, also manifest in subcortex, and highlight the value of using naturalistic stimuli to probe visual function.

neuroscience↗

bioRxiv2024

A sensorimotor-association axis of thalamocortical connection development

Human cortical development follows a sensorimotor-to-association sequence during childhood and adolescence1-6. The brains capacity to enact this sequence over decades indicates that it relies on intrinsic mechanisms to regulate inter-regional differences in the timing of cortical maturation, yet regulators of human developmental chronology are not well understood. Given evidence from animal models that thalamic axons modulate windows of cortical plasticity7-12, here we evaluate the overarching hypothesis that structural connections between the thalamus and cortex help to coordinate cortical maturational heterochronicity during youth. We first introduce, cortically annotate, and anatomically validate a new atlas of human thalamocortical connections using diffusion tractography. By applying this atlas to three independent youth datasets (ages 8-23 years; total N = 2,676), we reproducibly demonstrate that thalamocortical connections develop along a maturational gradient that aligns with the cortexs sensorimotor-association axis. Associative cortical regions with thalamic connections that take longest to mature exhibit protracted expression of neurochemical, structural, and functional markers indicative of higher circuit plasticity as well as heightened environmental sensitivity. This work highlights a central role for the thalamus in the orchestration of hierarchically organized and environmentally sensitive windows of cortical developmental malleability.

neuroscience↗

bioRxiv2023

Movies reveal the fine-grained organization of infant visual cortex

Studying infant minds with movies is a promising way to increase engagement relative to traditional tasks. However, the spatial specificity and functional significance of movie-evoked activity in infants remains unclear. Here we investigated what movies can reveal about the organization of the infant visual system. We collected fMRI data from 15 awake infants and toddlers aged 5-23 months who attentively watched a movie. The activity evoked by the movie reflected the functional profile of visual areas. Namely, homotopic areas from the two hemispheres responded similarly to the movie, whereas distinct areas responded dissim-ilarly, especially across dorsal and ventral visual cortex. Moreover, visual maps that typi-cally require time-intensive and complicated retinotopic mapping could be predicted, albeit imprecisely, from movie-evoked activity in both data-driven analyses (i.e., independent com-ponent analysis) at the individual level and by using functional alignment into a common low-dimensional embedding to generalize across participants. These results suggest that the infant visual system is already structured to process dynamic, naturalistic information and that fine-grained cortical organization can be discovered from movie data.

neuroscience↗

bioRxiv2020

Retinotopic organization of visual cortex in human infants

Vision develops rapidly during infancy, yet how visual cortex is organized during this period is unclear. One possibility is that the retinotopic organization of visual cortex emerges gradually as perceptual abilities improve. This may result in a hierarchical maturation of visual areas from striate to extrastriate cortex. Another possibility is that retinotopic organization is present from early infancy. This early maturation of area boundaries and tuning could scaffold further developmental changes. Here we test the functional maturity of infant visual cortex by performing retinotopic mapping with fMRI. Infants aged 5-23 months had retinotopic maps, with alternating preferences for vertical and horizontal meridians indicative of area boundaries from V1 to V4, and an orthogonal gradient of preferences from high to low spatial frequencies indicative of growing receptive field sizes. Although present in the youngest infants, these retinotopic maps showed subtle agerelated changes, suggesting that early maturation undergoes continued refinement.

neuroscience↗

bioRxiv2018

The HCP 7T Retinotopy Dataset

About a quarter of human cerebral cortex is dedicated mainly to visual processing. The large-scale organization of visual cortex can be measured with functional magnetic resonance imaging (fMRI) while subjects view spatially modulated visual stimuli, also known as retinotopic mapping. One of the datasets collected by the Human Connectome Project (HCP) involved ultra-high-field (7 Tesla) fMRI retinotopic mapping in 181 healthy young adults (1.6-mm resolution), yielding the largest freely available collection of retinotopy data. Here, we describe the experimental paradigm and the results of model-based analysis of the fMRI data. These results provide estimates of population receptive field position and size. Our analyses include both results from individual subjects as well as results obtained by averaging fMRI time-series across subjects at each cortical and subcortical location and then fitting models. Both the group-average and individual-subject results reveal robust signals across much of the brain, including occipital, temporal, parietal, and frontal cortex as well as subcortical areas. The group-average results agree well with previously published parcellations of visual areas. In addition, split-half analyses show strong within-subject reliability, further demonstrating the high quality of the data. We make publicly available the analysis results for individual subjects and the group average, as well as associated stimuli and analysis code. These resources provide an opportunity for studying fine-scale individual variability in cortical and subcortical organization and the properties of high-resolution fMRI. In addition, they provide a set of observations that can be compared with other HCP measures acquired in these same participants.

neuroscience↗

bioRxiv2017

Retinotopic Organization of Scene Areas in Macaque Inferior Temporal Cortex

Primates have specialized domains in inferior temporal (IT) cortex that are responsive to particular image categories. Though IT traditionally has been regarded as lacking retinotopy, several recent studies in monkeys have shown that retinotopic maps extend to face patches along the lower bank of the superior temporal sulcus (STS) in IT cortex. Here, we confirm the presence of visual field maps within and around the lower bank of the STS and extend these prior findings to scene-selective cortex in the ventral-most regions of IT. Within the occipito-temporal sulcus (OTS), we identified two retinotopic areas, OTS1 and OTS2. The polar angle representation of OTS2 was a mirror reversal of the OTS1 representation. These regions contained representations of the contralateral periphery and were selectively active for scene vs. face, body, or object images. The extent of this retinotopy parallels that in humans and shows that the organization of the scene network is preserved across primate species. In addition retinotopic maps were identified in dorsal extrastriate, posterior parietal, and frontal cortex as well as the thalamus, including both the LGN and pulvinar. Taken together, it appears that most, if not all, of the macaque visual system contains organized representations of visual space.\n\nSIGNIFICANCE STATEMENTPrimates have specialized domains in inferior temporal (IT) cortex that are responsive to particular image categories. Though retinotopic maps are considered a fundamental organizing principle of posterior visual cortex, IT traditionally has been regarded as lacking retinotopy. Recent imaging studies have demonstrated the presence of several visual field maps within lateral IT. Using neuroimaging, we found multiple representations of visual space within ventral IT cortex of macaques that included scene-selective IT cortex. The scene domains were biased towards the peripheral visual field. These data demonstrate the prevalence of visual field maps throughout the primate visual system, including late stages in the ventral visual hierarchy, and support the idea that domains representing different categories are biased towards different parts of the visual field.

neuroscience↗