Neuroscience and Neurobiology Commons^™

Using Deep Features To Predict Where People Look, Matthias Kümmerer, Matthias Bethge

MODVIS Workshop

When free-viewing scenes, the first few fixations of human observers are driven in part by bottom-up attention. We seek to characterize this process by extracting all information from images that can be used to predict fixation densities (Kuemmerer et al, PNAS, 2015). If we ignore time and observer identity, the average amount of information is slightly larger than 2 bits per image for the MIT 1003 dataset. The minimum amount of information is 0.3 bits and the maximum 5.2 bits. Before the rise of deep neural networks the best models were able to capture 1/3 of this information on average. …

Modelling Short-Latency Disparity-Vergence Eye Movements Under Dichoptic Unbalanced Stimulation, Agostino Gibaldi, Guido Maiello, Peter J. Bex, Silvio P. Sabatini

MODVIS Workshop

Vergence eye movements align the optical axes of our two eyes onto an object of interest, thus facilitating the binocular summation of the images projected onto the left and the right retinae into a single percept. Both the computational substrate and the functional behaviour of binocular vergence eye movements have been the topic of in depth investigation. Here, we attempt to bring together what is known about computation and function of vergence mechanism. To this aim, we evaluated of a biologically inspired model of horizontal and vertical vergence control, based on a network of V1 simple and complex cells. The …

Learning Object Representations For Modeling Attention In Real World Scenes, Alex Schwarz, Frederik Beuth, Fred H. Hamker

MODVIS Workshop

Models of visual attention have been rarely used in real world tasks as they have been typically developed for psychophysical setups using simple stimuli. Thus, the question remains how objects must be represented to allow such models an operation in real world scenarios. We have previously presented an attention model capable of operating on real-world scenes (Beuth, F., and Hamker, F. H. 2015, NCNC, which is a successor of Hamker, F. H., 2005, Cerebral Cortex), and show here how its object representations have been learned. We have used a learning rule based on temporal continuity (Földiák, P., 1991, Neural Computation) …

Axonal Transport And Life Cycle Of Mitochondria In Parkinson's Disease Model, Hyun Sung

Open Access Dissertations

In neurons, normal distribution and selective removal of mitochondria are essential for preserving compartmentalized cellular function. Parkin, an E3 ubiquitin ligase associated with familial Parkinson’s disease, has been implicated in mitochondrial dynamics and removal. However, it is not clear how Parkin plays a role in mitochondrial turnover in vivo, and whether the mature neurons possess a compartmentalized Parkin-dependent mitochondrial life cycle. Using the live Drosophila nervous system, here, I investigate the involvement of Parkin in mitochondrial dynamics; organelle distribution, morphology and removal. Parkin deficient animals displayed less number of axonal mitochondria without disturbing organelle motility behaviors, morphology and metabolic state. …

Consonant Discrimination In The Inferior Colliculus Of Young And Aged Rats, Christopher S. Soverns

Open Access Theses

Complex acoustic stimuli are thoroughly encoded and processed along the primary auditory pathway to give reliable and relevant information about the environment, and elucidating the neural coding mechanisms is essential to informing clinical attempts to combat auditory dysfuntion. Receiving a uniquely diverse set of ascending and descending inputs, the inferior colliculus (IC) is a site of intricate temporal processing. In this work, natural and modified human speech is used to investigate discrimination of voice onset time (VOT) in the spiking output of IC neurons. A template-matching classification model is proposed in which single stimulus presentation responses are correlated with aggregate …

The Effect Of Voluntary Binge Caffeine And Ethanol Coexposure On Neurobehavioral Sensitivity To Cocaine In Male C57bl/6j Mice, Brandon M. Fritz

Open Access Dissertations

Recently, the co-consumption of highly caffeinated energy drinks and alcohol has become a public health concern. Consumption of these beverages has been linked to a wide variety negative consequences including alcohol poisoning, driving under the influence, physical harm, and sexual violence. The more protracted consequences of caffeinated alcohol consumption have received very little attention, however. Some evidence suggests that individuals that frequently consume energy drinks mixed with alcohol are more likely to develop an alcohol use disorder. Interestingly, both caffeine and alcohol use alone have been linked to polydrug abuse. It is therefore of interest whether combined caffeine and alcohol …

Characterization Of Cu-Rich Aggregates In Neurogenic Niches Of The Rodent Brain By X-Ray Fluorescence Microscopy, Brendan T. Sullivan

Open Access Dissertations

Copper is an essential element in the brain playing several critical roles ranging from neurotransmitter synthesis to ATP production. As Cu is typically present in micromolar concentrations and has a spatially capricious distribution in the brain, determining concentrations has historically been challenging. X-ray fluorescence microscopy (XRF) offers excellent spatial resolution (down to 30~nm) and detection limits (sub parts per million), making it an excellent tool for analyzing metal distributions in the brain. Using XRF, it is demonstrated that Cu-rich aggregates with concentrations in the hundreds of millimolar are present in the subventricular zone of rats and mice. As the subventricular …

Characterizing The Rogfp2-Orp1 Fluorescent Biosensor For Detecting Oxidative Stress In Mammalian Cells, Sara A. Doan, Stevie Norcross, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Parkinson’s disease is a neurodegenerative disease involving the death of neurons in the substantia nigra and loss of the neurotransmitter, dopamine. The disease leads to progressive loss of motor control. Exact causes and mechanisms by which Parkinson’s disease proceeds are unknown, however, previous experiments determine oxidative stress in mitochondria as a factor that results in cell death. Strategies have been implemented to generate fluorescent biosensors to monitor reactive oxygen species (ROS) concentrations while simultaneously measuring the spatiotemporal distribution and correlation between the ROS, cellular function and organelle. Orp1, an enzyme found in yeast, is a sensitive oxidizing species and when …

A Screen To Identify Saga-Activated Genes That Are Required For Proper Photoreceptor Axon Targeting In Drosophila Melanogaster, Kaelan J. Brennan, Vikki M. Weake, Jingqun Q. Ma

The Summer Undergraduate Research Fellowship (SURF) Symposium

The inherited human genetic disease spinocerebellar ataxia type 7 (SCA7) is characterized by progressive neurodegeneration and visual impairment that ultimately leads to blindness. SCA7 results from a mutation in the human ATXN7 gene that causes an expansion of polyglutamine tracts in this gene’s corresponding protein. Human ATXN7 protein serves as a component of the deubiquitylase (DUB) module of the large, multi-subunit complex Spt-Ada-Gcn acetyltransferase, or SAGA. SAGA is a transcriptional coactivator and histone modifier that functions to deubiquitylate histone H2B and allow for transcription of SAGA-mediated genes to occur. In Drosophila, mutations in SAGA DUB’s Nonstop and sgf11 components …

Analysis Of Mitochondrial Turnover In Neuromuscular Junctions Of Parkin Mutants, Kenny Nguyen, Hyun Sung, Peter J. Hollenbeck

The Summer Undergraduate Research Fellowship (SURF) Symposium

The accumulation of dysfunctional or damaged mitochondria in neurons has been linked to the pathogenesis of many neurodegenerative diseases, such as Parkinson’s disease. It has been proposed that proteins PINK1 and Parkin regulate mitochondrial quality control by selectively targeting depolarized mitochondria for autophagic degradation, a process known as mitophagy. Though previously analyzed in the cell bodies and axons of neurons, the role of the PINK1/Parkin pathway in the synapse is unclear, and it is not known whether mitochondrial turnover occurs in the neuromuscular junctions (NMJs). To study this, intact Drosophila nervous systems were analyzed in vivo by performing gentle dissections …

Competitive Tuning Of Calmodulin Target Protein Activation Drives E-Ltp Induction In Ca1 Hippocampal Neurons, Daniel R. Romano, Tamara L. Kinzer-Ursem

The Summer Undergraduate Research Fellowship (SURF) Symposium

A number of neurological disorders are caused by disruptions in dynamic neuronal connections called synapses. Normally, electrical activity between neurons activates protein cascades that cause long-lasting, localized changes in the structure and molecular composition of synapses. These changes either increase or decrease the strength of synaptic connections, leading to long-term-potentiation (LTP) or long-term-depression (LTD), respectively. The protein cascades responsible for this synaptic plasticity are initiated in a stimulus-dependent manner by the Ca²⁺ sensor calmodulin (CaM). Ultimately, it is disruptions within these signaling pathways that cause disease. Traditionally, these protein networks are studied in the laboratory, but limitations in existing …

Behavioral Outputs Of Fragile-X Autistic Mice Exposed To Open-Field, Randomized, Short-Term Visual Stimuli, Nicholas M. Dicola, Alexander A. Chubykin

The Summer Undergraduate Research Fellowship (SURF) Symposium

Animal models of different neurological disorders are required for studying the pathophysiology of these diseases, and for potential development of pharmacological and behavioral treatments. The scientific community often uses mouse models for behavior studies due to their powerful genetic tools and low cost. However, subjective measurement techniques are often used when analyzing mice for behavioral traits which often results in discrepancies in results. An automated tracking software would aim to eliminate these discrepancies and subjective analysis. This lab has developed a software program which offered an ability to automatically collect open-field behavioral data with simultaneous on-line analysis. Python, an open …

Susceptibility Of Parkinson’S Disease Following Mild Blast Traumatic Brain Injury, Glen Howel Galicia Acosta

Open Access Theses

Blast injury-induced neurotrauma (BINT) is steadily increasing in prevalence due to escalated terror activity and constitutes the signature injury associated with current military conflicts. BINT produces significant neurological deficiencies and there is a growing concern that the injury may produce long-term consequences that affect the resilience and the performance of soldiers. One of the potential consequences is an increased susceptibility to Parkinson's disease (PD). A vital goal aimed at curtailing the post-deployment long-term consequences of blast injury-induced neurotrauma is to further our knowledge of pathogenic mechanisms responsible for the escalation of post injury diseases. The purpose of this project is …

Characterizing Receptive Field Selectivity In Area V2, Corey M. Ziemba, Robbe Lt Goris, J Anthony Movshon, Eero P. Simoncelli

MODVIS Workshop

The computations performed by neurons in area V1 are reasonably well understood, but computation in subsequent areas such as V2 have been more difficult to characterize. When stimulated with visual stimuli traditionally used to investigate V1, such as sinusoidal gratings, V2 neurons exhibit similar selectivity (but with larger receptive fields, and weaker responses) relative to V1 neurons. However, we find that V2 responses to synthetic stimuli designed to produce naturalistic patterns of joint activity in a model V1 population are more vigorous than responses to control stimuli that lacked this naturalistic structure (Freeman, et. al. 2013). Armed with this signature …

‘Edge’ Integration Explains Contrast And Assimilation In A Gradient Lightness Illusion, Michael E. Rudd

MODVIS Workshop

In the ‘phantom’ illusion (Galmonte, Soranzo, Rudd, & Agostini, submitted), either an incremental or a decremental target, when surrounded by a luminance gradient, can to be made to appear as an increment or a decrement, depending on the gradient width. For wide gradients, incremental targets appear as increments and decremental targets appear as decrements. For narrow gradients, the reverse is true. Here, I model these phenomena with a two-stage neural lightness theory (Rudd, 2013, 2014) in which local steps in log luminance are first encoded by oriented spatial filters operating on a log-transformed version of the image; then the filter …

Time-Lapse Statistics Of Cone Signals From Natural Scenes, David H. Foster, Kinjiro Amano, Sérgio M C Nascimento

MODVIS Workshop

In the natural world, the spectrum and geometry of the illumination from the sun and sky vary over the day. These geometric changes make it especially difficult to extract from the reflected light invariant signals for surface color perception. The aim of this study was to test the utility of certain combinations of retinal cone excitations, in particular, spatial cone-excitation ratios, known to be approximately invariant under non-geometric changes in illumination. Hyperspectral radiance images were acquired at roughly hourly intervals in four outdoor scenes in the Minho region of Portugal. Spatial resolution of the camera was 1344×1024 pixels. Peak-transmission wavelength …

The Bounded Log-Odds Model Of Frequency And Probability Distortion, Hang Zhang, Laurence T. Maloney

MODVIS Workshop

No abstract provided.

Putting Saliency In Its Place, John K. Tsotsos

MODVIS Workshop

The role of attention and the place within the visual processing stream where the concept of saliency has been situated is critically examined by considering the experimental evidence and performing tests that link experiment to computation.

Towards A Unified Computational Model Of Contextual Interactions Across Visual Modalities, David A. Mély, Thomas Serre

MODVIS Workshop

The perception of a stimulus is largely determined by its surrounding. Examples abound from color (Land and McCann, 1971), disparity (Westheimer, 1986) and motion induction (Anstis and Casco, 2006) to orientation tilt effects (O’Toole and Wenderoth, 1976). Some of these phenomena have been studied individually using monkey neurophysiology techniques. In these experiments, a center stimulus is typically used to probe a cell’s classical “center” receptive field (cRF), whose activity is then modulated by an annular “surround” (extra-cRF) stimulus. While this center-surround integration (CSI) has been well characterized, a theoretical framework which unifies these different phenomena across visual modalities is lacking. …

A Conceptual Framework Of Computations In Mid-Level Vision, Jonas Kubilius, Johan Wagemans, Hans P. Op De Beeck

MODVIS Workshop

The goal of visual processing is to extract information necessary for a variety of tasks, such as grasping objects, navigating in scenes, and recognizing them. While ultimately these tasks might be carried out by separate processing pathways, they nonetheless share a common root in the early and intermediate visual areas. What representations should these areas develop in order to facilitate all of these higher-level tasks? Several distinct ideas have received empirical support in the literature so far: (i) boundary feature detection, such as edge, corner, and curved segment extraction; (ii) second-order feature detection, such as the difference in orientation or …

Binocular 3d Motion Perception As Bayesian Inference, Martin Lages, Suzanne Heron

MODVIS Workshop

The human visual system encodes monocular motion and binocular disparity input before it is integrated into a single 3D percept. Here we propose a geometric-statistical model of human 3D motion perception that solves the aperture problem in 3D by assuming that (i) velocity constraints arise from inverse projection of local 2D velocity constraints in a binocular viewing geometry, (ii) noise from monocular motion and binocular disparity processing is independent, and (iii) slower motions are more likely to occur than faster ones. In two experiments we found that instantiation of this Bayesian model can explain perceived 3D line motion direction under …

A Binocular Model For Motion Integration In Mt Neurons, Pamela M. Baker, Wyeth Bair

MODVIS Workshop

Processing of visual motion by neurons in MT has long been an active area of study, however circuit models detailing the computations underlying binocular integration of motion signals remains elusive. Such models are important for studying the visual perception of motion in depth (MID), which involves both frontoparallel (FP) visual motion and binocular signal integration. Recent studies (Czuba et al. 2014, Sanada and DeAngelis 2014) have shown that many MT neurons are MID sensitive, contrary to the prevailing view (Maunsell and van Essen, 1983). These novel data are ideal for constraining models of binocular motion integration in MT. We have …

A Critical Evaluation Of Computational Mechanisms Of Binocular Disparity Processing, Junkyung Kim, David A. Mély, Thomas Serre

MODVIS Workshop

The past decades of research in visual neuroscience have generated a large and disparate body of literature on the computation of binocular disparity in the primary visual cortex. Models have been proposed to describe specific phenomena, yet we lack a theoretical framework which is grounded in neurophysiology and also explains the effectiveness of disparity computation. Here, we examine neural circuits that are thought to play an important role in the computation of binocular disparity. Starting with the binocular energy model (Ohzawa et al. 1990), we consider plausible extensions which include suppressive mechanisms from units tuned to different phase disparities (Tanabe …

Modeling Shape Representation In Area V4, Wyeth Bair, Dina Popovkina, Abhishek De, Anitha Pasupathy

MODVIS Workshop

Our model builds on a convolutional-style neural network with hierarchical stages representing processing steps in the ventral visual pathway. It was designed to capture the translation-invariance and shape-selectivity of neurons in area V4. The model uses biologically plausible linear filters at the front end, normalization and sigmoidal nonlinear activation functions. The max() function is used to generate translation invariance.

A Recurrent Multilayer Model With Hebbian Learning And Intrinsic Plasticity Leads To Invariant Object Recognition And Biologically Plausible Receptive Fields, Michael Teichmann, Fred H. Hamker

MODVIS Workshop

Much effort has been spent to develop biologically plausible models for different aspects of the processing in the visual cortex. However, most of these models are not investigated with respect to the functionality of the neural code for the purpose of object recognition comparable to the framework of deep learning in the machine learning community.
We developed a model of V1 and V2 based on anatomical evidence of the layered architecture, using excitatory and inhibitory neurons where the connectivity to each neuron is learned in parallel. We address learning by three different mechanisms of plasticity: intrinsic plasticity, Hebbian learning with …

A Computational Model To Account For Dynamics Of Spatial Updating Of Remembered Visual Targets Across Slow And Rapid Eye Movements, Yalda Mohsenzadeh, J. Douglas Crawford

MODVIS Workshop

Despite the ever-changing visual scene on the retina between eye movements, our perception of the visual world is constant and unified. It is generally believed that this space constancy is due to the brain’s ability of spatial updating. Although many efforts have been made to discover the mechanism underlying spatial updating across eye movements, still there are many unanswered questions about the neuronal mechanism of this phenomenon.

We developed a state space model for updating gaze-centered spatial information. To explore spatial updating, we considered two kinds of eye movements, saccade and smooth pursuit. The inputs to our proposed model are: …

A Model Of Repetitive Microsaccades, Coupled With Pre-Microsaccadic Changes In Vision, Is Sufficient To Account For Both Attentional Capture And Inhibition Of Return In Posner Cueing, Ziad M. Hafed, Xiaoguang Tian

MODVIS Workshop

When a cue is presented at a location, orienting efficacy towards that location is improved relative to other locations (“attentional capture”), but only briefly; a mere few hundred milliseconds later, orienting incurs large costs. These costs have been classically termed “inhibition of return” (IOR), alluding to voluntary, cognitive strategies avoiding perseverance at one location. However, despite this popular hypothesis, the origins of both attentional capture and IOR remain elusive. Here we show that both of these phenomena can be accounted for by a single concept of oculomotor rhythmicity, and one that involves the entire gamut of saccadic activity including microsaccades. …

Object Recognition And Visual Search With A Physiologically Grounded Model Of Visual Attention, Frederik Beuth, Fred H. Hamker

MODVIS Workshop

Visual attention models can explain a rich set of physiological data (Reynolds & Heeger, 2009, Neuron), but can rarely link these findings to real-world tasks. Here, we would like to narrow this gap with a novel, physiologically grounded model of visual attention by demonstrating its objects recognition abilities in noisy scenes.

To base the model on physiological data, we used a recently developed microcircuit model of visual attention (Beuth & Hamker, in revision, Vision Res) which explains a large set of attention experiments, e.g. biased competition, modulation of contrast response functions, tuning curves, and surround suppression. Objects are represented by …

Modeling Visual Features To Recognize Biological Motion: A Developmental Approach, Giulio Sandini, Nicoletta Noceti, Alessia Vignolo, Alessandra Sciutti, Francesco Rea, Alessandro Verri, Francesca Odone

MODVIS Workshop

In this work we deal with the problem of designing and developing computational vision models – comparable to the early stages of the human development – using coarse low-level information.

More specifically, we consider a binary classification setting to characterize biological movements with respect to non-biological dynamic events. To this purpose, our model builds on top of the optical flow estimation, and abstract the representation to simulate the limited amount of visual information available at birth. We take inspiration from known biological motion regularities explained by the Two-Thirds Power Law, and design a motion representation that includes different low-level features, …

Cerebrovascular Reactivity Alterations Due To Subconcussive Repetitive Head Trauma In Asymptomatic High School Football Players, Chetas Joshi

Open Access Theses

Chronic neurological damage as a result of chronic repetitive head trauma is a major concern for football athletes today. Repetitive concussions have been linked to many neurological disorders. Recently, it has been reported that repetitive subconcussive events can contribute to long-term neurodegeneration. For these reasons, it is important to understand the effect repetitive subconcussive head trauma has on brain health in young athletes. Past research has demonstrated that cerebrovascular reactivity (CVR), an important mediator of cerebrovascular regulation, is impaired following mild traumatic brain injury (mTBI). This impairment increases susceptibility to secondary injury following mTBI. In this study, Breath-Hold (BH) task …