Deriving the cone fundamentals: a subspace intersection method.

Two ideas, proposed by Thomas Young and James Clerk Maxwell, form the foundations of colour science: (i) three types of retinal receptors encode light under daytime conditions, and (ii) colour matching experiments establish the critical spectral properties of this encoding. Experimental quantification of these ideas is used in international colour standards. However, for many years, the field did not reach consensus on the spectral properties of the biological substrate of colour matching: the spectral sensitivity of the cone fundamentals.

Reproducible Tract Profiles 2 (RTP2) suite, from diffusion MRI acquisition to clinical practice and research.

Diffusion MRI is a complex technique, where new discoveries and implementations occur at a fast pace. The expertise needed for data analyses and accurate and reproducible results is increasingly demanding and requires multidisciplinary collaborations. In the present work we introduce Reproducible Tract Profiles 2 (RTP2), a set of flexible and automated methods to analyze anatomical MRI and diffusion weighted imaging (DWI) data for reproducible tractography.

Measuring brain beats: Cardiac-aligned fast functional magnetic resonance imaging signals.

Blood and cerebrospinal fluid (CSF) pulse and flow throughout the brain, driven by the cardiac cycle. These fluid dynamics, which are essential to healthy brain function, are characterized by several noninvasive magnetic resonance imaging (MRI) methods. Recent developments in fast MRI, specifically simultaneous multislice acquisition methods, provide a new opportunity to rapidly and broadly assess cardiac-driven flow, including CSF spaces, surface vessels and parenchymal vessels.

Ray-transfer functions for camera simulation of 3D scenes with hidden lens design.

Combining image sensor simulation tools with physically based ray tracing enables the design and evaluation (soft prototyping) of novel imaging systems. These methods can also synthesize physically accurate, labeled images for machine learning applications. One practical limitation of soft prototyping has been simulating the optics precisely: lens manufacturers generally prefer to keep lens design confidential.

Visual encoding: Principles and software.

For more than two centuries scientists and engineers have worked to understand and model how the eye encodes electromagnetic radiation (light). We now understand the principles of how light is transmitted through the optics of the eye and encoded by retinal photoreceptors and light-sensitive neurons. In recent years, new instrumentation has enabled scientists to measure the specific parameters of the optics and photoreceptor encoding.

Simulations of fluorescence imaging in the oral cavity.

We describe an end-to-end image systems simulation that models a device capable of measuring fluorescence in the oral cavity. Our software includes a 3D model of the oral cavity and excitation-emission matrices of endogenous fluorophores that predict the spectral radiance of oral mucosal tissue. The predicted radiance is transformed by a model of the optics and image sensor to generate expected sensor image values.

Population Receptive Field Shapes in Early Visual Cortex Are Nearly Circular.

The visual field region where a stimulus evokes a neural response is called the receptive field (RF). Analytical tools combined with functional MRI (fMRI) can estimate the RF of the population of neurons within a voxel. Circular population RF (pRF) methods accurately specify the central position of the pRF and provide some information about the spatial extent (diameter) of the RF.

Data-science ready, multisite, human diffusion MRI white-matter-tract statistics.

The white matter tracts in the living human brain are critical for healthy function, and the diffusion MRI measured in these tracts is correlated with diverse behavioral measures. The technical skills required to analyze diffusion MRI data are complex: data acquisition requires MRI sequence development and acquisition expertise, analyzing raw-data into meaningful summary statistics requires computational neuroimaging and neuroanatomy expertise. The human white matter study field will advance faster if the tract summaries are available in plain data-science-ready format for non-diffusion MRI experts, such as statisticians, computer graphic researchers or data scientists in general.

V1 Projection Zone Signals in Human Macular Degeneration Depend on Task Despite Absence of Visual Stimulus.

Identifying the plastic and stable components of the visual cortex after retinal loss is an important topic in visual neuroscience and neuro-ophthalmology. Humans with juvenile macular degeneration (JMD) show significant blood-oxygen-level-dependent (BOLD) responses in the primary visual area (V1) lesion projection zone (LPZ), despite the absence of the feedforward signals from the degenerated retina. Our previous study reported that V1 LPZ responds to full-field visual stimuli during the one-back task (OBT), not during passive viewing, suggesting the involvement of task-related feedback signals.

A computational observer model of spatial contrast sensitivity: Effects of photocurrent encoding, fixational eye movements, and inference engine.

We have recently shown that the relative spatial contrast sensitivity function (CSF) of a computational observer operating on the cone mosaic photopigment excitations of a stationary retina has the same shape as human subjects. Absolute human sensitivity, however, is 5- to 10-fold lower than the computational observer. Here we model how additional known features of early vision affect the CSF: fixational eye movements and the conversion of cone photopigment excitations to cone photocurrents (phototransduction).

A validation framework for neuroimaging software: The case of population receptive fields.

Neuroimaging software methods are complex, making it a near certainty that some implementations will contain errors. Modern computational techniques (i.e.

The human connectome project for disordered emotional states: Protocol and rationale for a research domain criteria study of brain connectivity in young adult anxiety and depression.

Through the Human Connectome Project (HCP) our understanding of the functional connectome of the healthy brain has been dramatically accelerated. Given the pressing public health need, we must increase our understanding of how connectome dysfunctions give rise to disordered mental states. Mental disorders arising from high levels of negative emotion or from the loss of positive emotional experience affect over 400 million people globally.

Simultaneous Surface Reflectance and Fluorescence Spectra Estimation.

There is widespread interest in estimating the fluorescence properties of natural materials in an image. However, the separation between reflected and fluoresced components is difficult, because it is impossible to distinguish reflected and fluoresced photons without controlling the illuminant spectrum. We show how to jointly estimate the reflectance and fluorescence from a single set of images acquired under multiple illuminants.

Ray tracing 3D spectral scenes through human optics models.

Scientists and engineers have created computations and made measurements that characterize the first steps of seeing. ISETBio software integrates such computations and data into an open-source software package. The initial ISETBio implementations modeled image formation (physiological optics) for planar or distant scenes.

Replication and generalization in applied neuroimaging.

There is much interest in translating neuroimaging findings into meaningful clinical diagnostics. The goal of scientific discoveries differs from clinical diagnostics. Scientific discoveries must replicate under a specific set of conditions; to translate to the clinic we must show that findings using purpose-built scientific instruments will be observable in clinical populations and instruments.

Computational-observer analysis of illumination discrimination.

The spectral properties of the ambient illumination provide useful information about time of day and weather. We study the perceptual representation of illumination by analyzing measurements of how well people discriminate between illuminations across scene configurations. More specifically, we compare human performance to a computational-observer analysis that evaluates the information available in the isomerizations of cone photopigment in a model human photoreceptor mosaic.

A Conversation with Jacob Nachmias.

We are sad to report that Professor Jacob (Jack) Nachmias passed away on March 2, 2019. Nachmias was born in Athens, Greece, on June 9, 1928. To escape the Nazis, he and his family came to the United States in 1939.

iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology.

The Brain Imaging Data Structure (BIDS) is a community-driven specification for organizing neuroscience data and metadata with the aim to make datasets more transparent, reusable, and reproducible. Intracranial electroencephalography (iEEG) data offer a unique combination of high spatial and temporal resolution measurements of the living human brain. To improve internal (re)use and external sharing of these unique data, we present a specification for storing and sharing iEEG data: iEEG-BIDS.

A computational-observer model of spatial contrast sensitivity: Effects of wave-front-based optics, cone-mosaic structure, and inference engine.

We present a computational-observer model of the human spatial contrast-sensitivity function based on the Image Systems Engineering Toolbox for Biology (ISETBio) simulation framework. We demonstrate that ISETBio-derived contrast-sensitivity functions agree well with ones derived using traditional ideal-observer approaches, when the mosaic, optics, and inference engine are matched. Further simulations extend earlier work by considering more realistic cone mosaics, more recent measurements of human physiological optics, and the effect of varying the inference engine used to link visual representations to psychophysical performance.

Simulation of visual perception and learning with a retinal prosthesis.

Objective: The nature of artificial vision with a retinal prosthesis, and the degree to which the brain can adapt to the unnatural input from such a device, are poorly understood. Therefore, the development of current and future devices may be aided by theory and simulations that help to infer and understand what prosthesis patients see.

Approach: A biologically-informed, extensible computational framework is presented here to predict visual perception and the potential effect of learning with a subretinal prosthesis.

The ENGAGE study: Integrating neuroimaging, virtual reality and smartphone sensing to understand self-regulation for managing depression and obesity in a precision medicine model.

Precision medicine models for personalizing achieving sustained behavior change are largely outside of current clinical practice. Yet, changing self-regulatory behaviors is fundamental to the self-management of complex lifestyle-related chronic conditions such as depression and obesity - two top contributors to the global burden of disease and disability. To optimize treatments and address these burdens, behavior change and self-regulation must be better understood in relation to their neurobiological underpinnings.

Diagnosing the Neural Circuitry of Reading.

We summarize the current state of knowledge of the brain's reading circuits, and then we describe opportunities to use quantitative and reproducible methods for diagnosing these circuits. Neural circuit diagnostics-by which we mean identifying the locations and responses in an individual that differ significantly from measurements in good readers-can help parents and educators select the best remediation strategy. A sustained effort to develop and share diagnostic methods can support the societal goal of improving literacy.

Learning the Image Processing Pipeline.

Many creative ideas are being proposed for image sensor designs, and these may be useful in applications ranging from consumer photography to computer vision. To understand and evaluate each new design, we must create a corresponding image processing pipeline that transforms the sensor data into a form, that is appropriate for the application. The need to design and optimize these pipelines is time-consuming and costly.

The field of view available to the ventral occipito-temporal reading circuitry.

Skilled reading requires rapidly recognizing letters and word forms; people learn this skill best for words presented in the central visual field. Measurements over the last decade have shown that when children learn to read, responses within ventral occipito-temporal cortex (VOT) become increasingly selective to word forms. We call these regions the VOT reading circuitry (VOTRC).

In vivo evidence of functional and anatomical stripe-based subdivisions in human V2 and V3.

Visual cortex contains a hierarchy of visual areas. The earliest cortical area (V1) contains neurons responding to colour, form and motion. Later areas specialize on processing of specific features.