Biology subjects

Martins, D. M.

Publications and source records attributed to Martins, D. M..

8 recordsLinked to original sources

bioRxiv2026

Temporally organized activity in mouse V1 encodes newly sampled visual content during free movement

Natural vision is continuously shaped by an animal's own movements, which determine what enters the visual system and when visual input changes. Gaze shifts are known to initiate a temporally structured sequence of activity in primary visual cortex (V1), but how the visual content sampled by each movement contributes to this sequence has remained unclear. We recorded visual input, eye and head movements, and V1 activity in freely moving mice, and asked how the visual content sampled on each gaze shift shapes the response. The magnitude of visual change induced by each gaze shift scaled the amplitude of responses according to each neuron's characteristic response profile, while movement amplitude alone did not reproduce this modulation in darkness, supporting a role of visual input in driving the sequence. Activity following gaze shifts reflected each neuron's spatial receptive field structure, and visual filters estimated under head-fixed conditions predicted the relative timing of spike responses during gaze shifts of freely moving animals, demonstrating that gaze shift responses encode visual information. At the population level, decoded V1 activity shifted toward the scene sampled after each gaze shift. Thus, across single-neuron, spatial, temporal, and population measures, V1 activity tracked the content of each sample beyond movement timing alone, indicating that gaze shifts act as sampling events that result in V1 encoding visual information in temporally ordered responses.

neuroscience↗

bioRxiv2026

Visualizing and sonifying neurodata (ViSoND) for enhanced observation

Neuroscience needs observation. Observation lets us evaluate data quality, judge whether models are biologically realistic, and generate new hypotheses. However, high-dimensional behavioral and neural data are too complex to be easily displayed and eye-tested. Computational methods can reduce the dimensionality of data and reveal statistically robust dynamical structure but often yield results that are difficult to relate back to the underlying biology. In addition, the choice of what parameters to quantify may not capture unexpectedly relevant aspects of the data. To supplement quantification with enhanced qualitative observation, we developed Visualization and Sonification of NeuroData (ViSoND), an open-source approach for displaying multiple data streams using video and sonification. Sonification is nothing new to neuroscience. Scientists have sonified their physiological preparations since Lord Adrians earliest recordings. We extend this tradition by mapping multiple physiological datastreams to musical notes using MIDI. Synchronizing MIDI to video provides an opportunity to watch an animals movement while listening to physiological signals such as action potentials. Here we provide two demonstrations of this approach. First, we used ViSoND to interpret behavioral structure revealed by a computational model trained on the breathing rhythms of freely behaving mice. Second, ViSoND revealed patterns of neural activity in mouse visual cortex corresponding to eye blinks, events that were previously filtered out of analysis. These use cases show that ViSoND can supplement quantitative rigor with observational interpretability. Additionally, ViSoND provides an accessible way to display data which may broaden the audience for communication of neuroscientific findings.

neuroscience↗

bioRxiv2025

The impact of the serotonergic psychedelic DOI on active vision in freely moving mice

Psychedelics offer a unique opportunity to investigate the neural mechanisms governing both normal and altered perceptual states, yet relatively little is known about their impact on visual processing at the level of neural coding, particularly in the context of active vision. Here we examined how the serotonergic psychedelic DOI (2,5-dimethoxy-4-iodoamphetamine) influences neural activity within the visual cortex (V1) of freely moving mice engaged in naturalistic vision. Previous work has demonstrated that, under normal conditions, gaze shifts trigger a temporal sequence in V1 that encodes visual information in a coarse-to-fine sequence. Here we found that DOI had a diverse and temporally dynamic impact on response amplitudes across this sequence -- while net population-level firing was modestly suppressed, individual neurons showed large increases or decreases in their gaze shift responses. Strikingly, this bidirectional modulation was correlated with gaze-shift response latency. DOI had mixed effects on short latency, low spatial frequency preferring neurons, but became increasingly suppressive across the sequence, ultimately suppressing nearly all long latency, high spatial frequency preferring neurons. These findings demonstrate how psychedelics disrupt naturalistic visual processing and support a framework in which visual hallucinations result from an imbalance in coarse and fine input integration during active vision. HighlightsO_LIWe recorded neural activity from V1 of freely moving mice before and after administration of the psychedelic DOI. C_LIO_LIDOI had diverse effects on visual response amplitude following a gaze shift, with some neurons increasing while others decreased. C_LIO_LIThe modulation of responses was temporally dynamic, shifting across the response sequence. C_LIO_LILonger latency neurons, which preferentially encode high spatial frequency information, were more consistently suppressed C_LIO_LITogether these effects result in a disruption of population response and coarse-to-fine processing, providing potential mechanisms for altered visual perception C_LI

neuroscience↗

bioRxiv2025

Neural dynamics in superior colliculus of freely moving mice

Vision is an active process that depends on head and eye movements to explore the visual environment. Superior colliculus (SC) is known for its role in generating these movements, as well as processing visual information, but has not been studied extensively during free movement in complex visual environments. To determine the impact of active vision, we recorded neural activity across the depth of SC during free movement while simultaneously recording eye and head position. We find that superficial SC (sSC) neurons respond to visual input following gaze-shifting saccadic movements, whereas deep SC (dSC) neurons respond to the movements themselves, as demonstrated by their sustained response in darkness. Additionally, we find motor responses in dSC are more correlated to head movements rather than eye movements. Furthermore, we compared sSC gaze shift responses to known gaze shift responses in primary visual cortex (V1), finding similarities in key response types, although the temporal sequences following gaze shifts differ between the regions. Our results demonstrate distinct visual processing differences between SC and V1 as well as highlighting the various roles SC plays during active vision. HighlightsO_LIWe recorded neural activity across the depths of superior colliculus (SC) in freely moving mice while measuring head and eye movements. C_LIO_LINeurons in mouse SC respond strongly to gaze shifts, and these responses differ between superficial (sSC) and deep (dSC) layers. C_LIO_LIsSC neurons respond primarily to the visual input during a saccadic movement. C_LIO_LIdSC neurons generally represent the head movement more than the eye movement, independent of visual input. C_LIO_LIWhile sSC gaze shift responses share similarities with V1 there are unique response profiles in SC that suggest differences in the role of visual processing between SC and V1 during free movement. C_LI

neuroscience↗

bioRxiv2022

A dynamic sequence of visual processing initiated by gaze shifts

Animals move their head and eyes as they explore and sample the visual scene. Previous studies have demonstrated neural correlates of head and eye movements in rodent primary visual cortex (V1), but the sources and computational roles of these signals are unclear. We addressed this by combining measurement of head and eye movements with high density neural recordings in freely moving mice. V1 neurons responded primarily to gaze shifts, where head movements are accompanied by saccadic eye movements, but not to head movements where compensatory eye movements stabilize gaze. A variety of activity patterns immediately followed gaze shifts, including units with positive, biphasic, or negative responses, and together these responses formed a temporal sequence following the gaze shift. These responses were greatly diminished in the dark for the vast majority of units, replaced by a uniform suppression of activity, and were similar to those evoked by sequentially flashed stimuli in head-fixed conditions, suggesting that gaze shift transients represent the temporal response to the rapid onset of new visual input. Notably, neurons responded in a sequence that matches their spatial frequency preference, from low to high spatial frequency tuning, consistent with coarse-to-fine processing of the visual scene following each gaze shift. Recordings in foveal V1 of freely gazing head-fixed marmosets revealed a similar sequence of temporal response following a saccade, as well as the progression of spatial frequency tuning. Together, our results demonstrate that active vision in both mice and marmosets consists of a dynamic temporal sequence of neural activity associated with visual sampling. HighlightsO_LIDuring free movement, neurons in mouse V1 respond to head movements that are accompanied by a gaze-shifting saccadic eye movement, but not a compensatory eye movement. C_LIO_LINeurons respond to gaze shifts with diverse temporal dynamics that form a sequence across the population, from early positive responses to biphasic and negative responses. C_LIO_LIIn darkness, most neurons show a uniform suppression following a gaze shift. C_LIO_LITemporal dynamics of responses correspond to a neurons temporal and spatial frequency preferences, consistent with a coarse-to-fine processing sequence. C_LIO_LIA similar temporal sequence following saccades is observed in foveal V1 of freely gazing head-fixed marmosets, demonstrating shared aspects of active visual processing across species. C_LI

neuroscience↗

bioRxiv2022

Joint coding of visual input and eye/head position in V1 of freely moving mice

SUMMARYVisual input to the brain during natural behavior is highly dependent on movements of the eyes, head, and body. Neurons in mouse primary visual cortex (V1) respond to eye and head movements, but how information about eye and head position is integrated with visual processing during free movement is unknown, since visual physiology is generally performed under head-fixation. To address this, we performed single-unit electrophysiology in V1 of freely moving mice while simultaneously measuring the mouses eye position, head orientation, and the visual scene from the mouses perspective. Based on these measures we were able to map spatiotemporal receptive fields during free movement, using a generalized linear model (GLM) that predicted the activity of V1 neurons based on gaze-corrected visual input. Furthermore, we found that a significant fraction of visually-responsive neurons showed tuning for eye position and head orientation. Incorporating these variables into the GLM revealed that visual and positional signals are integrated through a multiplicative mechanism in the majority of modulated neurons, consistent with computation via gain fields and nonlinear mixed selectivity. These results provide new insight into coding in mouse V1, and more generally provide a paradigm for performing visual physiology under natural conditions, including active sensing and ethological behavior. HIGHLIGHTSO_LINeurons in mouse V1 respond to both vision and self-motion, but it is unclear how these are combined. C_LIO_LIWe record neural activity in V1 concurrent with measurement of the visual input from the mouses perspective during free movement. C_LIO_LIThese data provide the first measurement of visual receptive fields in freely moving animals. C_LIO_LIWe show that many V1 neurons are tuned to eye position and head orientation, and these contribute a multiplicative gain on visual responses in the majority of modulated neurons. C_LI

neuroscience↗

bioRxiv2021

Distance estimation from monocular cues in an ethological visuomotor task

In natural contexts, sensory processing and motor output are closely coupled, which is reflected in the fact that many brain areas contain both sensory and movement signals. However, standard reductionist paradigms decouple sensory decisions from their natural motor consequences, and head-fixation prevents the natural sensory consequences of self-motion. In particular, movement through the environment provides a number of depth cues beyond stereo vision that are poorly understood. To study the integration of visual processing and motor output in a naturalistic task, we investigated distance estimation in freely moving mice. We found that mice use vision to accurately jump across a variable gap, thus directly coupling a visual computation to its corresponding ethological motor output. Monocular eyelid suture did not affect gap jumping success, thus mice can use cues that do not depend on binocular disparity and stereo vision. Under monocular conditions, mice altered their head positioning and performed more vertical head movements, consistent with a shift from using stereopsis to other monocular cues, such as motion or position parallax. Finally, optogenetic suppression of primary visual cortex impaired task performance under both binocular and monocular conditions when optical fiber placement was localized to binocular or monocular zone V1, respectively. Together, these results show that mice can use monocular cues, relying on visual cortex, to accurately judge distance. Furthermore, this behavioral paradigm provides a foundation for studying how neural circuits convert sensory information into ethological motor output.

neuroscience↗

bioRxiv2020

Quantifying multi-species microbial interactions in the larval zebrafish gut

The microbial communities resident in animal intestines are composed of multiple species that together play important roles in host development, health and disease. Due to the complexity of these communities and the difficulty of characterizing them in situ, the determinants of microbial composition remain largely unknown. Further, it is unclear for many multi-species consortia whether their species-level makeup can be predicted based on an understanding of pairwise species interactions, or whether higher-order interactions are needed to explain emergent compositions. To address this, we examine commensal intestinal microbes in larval zebrafish, initially raised germ-free to allow introduction of controlled combinations of bacterial species. Using a dissection and plating assay, we demonstrate the construction of communities of one to five bacterial species and show that the outcomes from the two-species competitions fail to predict species abundances in more complex communities. With multiple species present, inter-bacterial interactions become weaker and more cooperative, suggesting that higher-order interactions in the vertebrate gut may stabilize complex communities.

microbiology↗