About

James A. Simmons is a Professor of Biology whose laboratory specializes in the study of biological sonar systems in bats. His research primarily focuses on the big brown bat, Eptesicus fuscus, which emits ultrasonic, frequency-modulated echolocation sounds and demonstrates sophisticated real-time signal-processing techniques for auditory representation of echoes. The principal goal of his work is to understand how natural images are created in perception through neural reconstruction of the target scene by the bat's brain. His research areas include the auditory system, biosonar, echolocation, and hearing. Professor Simmons's contributions include advancing the understanding of how bats modulate pulse intervals to overcome range ambiguity in cluttered environments, modeling biosonar echo processing, and investigating neural responses related to target shape perception and clutter rejection. His work also explores the effects of environmental factors on echolocation behavior, the neural mechanisms underlying spatial memory, and the development of bio-inspired sonar models for high-resolution imaging. Through these efforts, he has significantly contributed to the fields of neurobiology, animal bioacoustics, and sensory processing, providing insights into the neural and behavioral mechanisms that enable bats to navigate and hunt with remarkable precision.

Research topics

• Computer Science
• Physics
• Optics
• Artificial Intelligence
• Acoustics
• Speech recognition
• Biology
• Biomedical engineering
• Telecommunications
• Materials science
• Medicine
• Medical physics

Selected publications

• Photon absorption remote sensing (PARS): comprehensive absorption imaging enabling label-free biomolecule characterization and mapping

  Scientific Reports · 2026-05-09

  articleOpen access

  Label-free optical absorption microscopy techniques continue to evolve as promising tools for label-free histopathological imaging of cells and tissues. However, critical challenges relating to specificity and contrast, as compared to current gold-standard methods continue to hamper adoption. This work introduces Photon Absorption Remote Sensing (PARS), a new absorption microscope modality, which simultaneously captures the dominant de-excitation processes following an absorption event. In PARS, radiative (auto-fluorescence) and non-radiative (photothermal and photoacoustic) relaxation processes are collected simultaneously, providing enhanced specificity to a range of biomolecules. As an example, a multiwavelength PARS system featuring UV (266 nm) and visible (532 nm) excitation is applied to imaging human skin, and murine brain tissue samples. It is shown that PARS can directly characterize, differentiate, and unmix, clinically relevant biomolecules inside complex tissues samples using established statistical processing methods. Gaussian mixture models (GMM) are used to characterize clinically relevant biomolecules (e.g., white, and gray matter) based on their PARS signals, while non-negative least squares (NNLS) is applied to map the biomolecule abundance in murine brain tissues, without stained ground truth images or deep-learning methods. PARS unmixing and abundance estimates are directly validated and compared against chemically stained ground truth images, and deep learning based-image transforms. Overall, it is found that the PARS unique and rich contrast may provide comprehensive, and otherwise inaccessible, label-free characterization of molecular pathology, representing a new source of data to develop AI and machine learning methods for diagnostics and visualization.

  PublisherDOI

• Performance of a random forest classifier on auditory brainstem responses to echo glint structure

  Proceedings of meetings on acoustics · 2025-01-01

  articleOpen accessSenior author
  PublisherDOI

• Cochlear representation of wideband biosonar sounds and the emergence of neural oscillations

  Hearing Research · 2025-04-07

  reviewOpen access1st authorCorresponding

  Echolocating big brown bats and bottlenose dolphins broadcast wideband ultrasonic echolocation calls in the baseband to sense their surroundings. Even though these species inhabit different media and emit echolocation calls with different spectra, both show similar perceptual acuity: They determine target range from echo delay, they detect changes in echo delay on a microsecond scale, and they perceive ultrasonic phase. These perceptual performances are too acute to understand on the basis of single neuron responses, and even neural population responses do not reach the required behavioral values. Here we propose two mechanisms that may contribute to temporal hyperacuity in these wideband echolocators. Structural imaging studies show that in both species the cochlea receives input from the middle ear at locations different from that seen in non-echolocating mammals. These unusual patterns of input might produce interference patterns in traveling waves along the basilar membrane, which in turn could facilitate detection of ultrasonic phase by producing low difference frequencies that may form a substrate for further neural processing into perception. The second mechanism is related to oscillations of evoked activity observed in the bat's inferior colliculus, which could create broadcast-echo interference patterns at the neural level. The resulting difference-frequency interference signals would be very sensitive to changes in echo delay and phase. Small changes in ultrasonic sounds thus could lead to much larger changes in neural response timing by magnifying echo time itself.

  PublisherDOI

• Echolocation calls of some bat species in western Uganda

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-15

  articleOpen access

  ABSTRACT With the rise of accessible recording technology, passive acoustic monitoring can be an affordable and rapid way to assess species richness, even when individual animals cannot be captured due to regulatory or practical obstacles. Motivated by the relative lack of data and in partnership with the local populace, we recorded echolocation calls of freely-flying bats across six locations in rural western Uganda using opportunistic passive acoustic recordings. Frequency-modulated echolocation calls were recorded at all six locations, while constant-frequency calls were recorded only at sites near entrances to caves. Preliminary species identifications were made using Kaleidoscope Pro, habitat distribution maps for Uganda, and by reference to published work. We make our acoustic recordings publicly available to serve as a resource for further explorations of the richness of bat species in Uganda.

  PublisherDOI

• Effect of Masking Secondary to the COVID-19 Pandemic on Pulmonary Rehabilitation Outcomes

  Journal of Cardiopulmonary Rehabilitation and Prevention · 2025-05-22

  article
  PublisherDOI

• 154. The impact of a novel whey protein concentrate (FXP™) on serum C-reactive protein and intestinal morphology of nursery pigs during a natural enteric health challenge

  Animal - science proceedings · 2025-08-01

  article
  PublisherDOI

• Investigating color dependence of neurovascular coupling in the healthy human retina using functional OCT

  2025-03-19

  article

  Neurovascular coupling in the human retina refers to the transient increase in the retinal blood flow (RBF) caused by an increased metabolic demand of the retinal neurons associated with the visual simulation of the retina. Retinal neurodegenerative diseases such as Glaucoma have been linked with decreased RBF, in addition to abnormalities in the elasticity of the blood vessels’ walls. In this study, a research-grade, high-resolution Functional OCT system is used to investigate flicker-stimulus-induced color dependence of neurovascular coupling in retinal blood vessels around the Optic Nerve Head (ONH).

  PublisherDOI

• Investigation of Non-Radiative Relaxation Dynamics Under Pulsed Excitation Using Photon Absorption Remote Sensing: A Proof-of-Principle Study in Mechanical Sensing

  ArXiv.org · 2025-02-27 · 1 citations

  preprintOpen access

  The mechanical properties of micro-scale bio-entities are fundamental for understanding their functions and pathological states. However, current methods for assessing elastic properties at single-particle level such as Brillouin and atomic force microscopies exhibit intrinsic limitations, including being often slow, having poor resolution, or involving complicated and invasive setups. In this study, we explore Photon Absorption Remote Sensing (PARS) microscopy as a unique solution for mechanical sensing of single micro-objects. PARS uses probe beam scattering/reflectivity measurements to capture non-radiative relaxation process following the absorption of a pulse of light by a micro-object. In particular, we demonstrate that, when operating at GHz-range bandwidth, PARS can trace the sub-nanosecond dynamics of non-radiative relaxation in individual micro-objects, capturing both photoacoustic (PA) pressure propagation and thermal diffusion. This GHz-range measurement, in conjunction with a developed descriptive model, enables the experimental extraction of a minimally distorted PA temporal profile. The PA temporal profile contain information on the ratio between the absorbing object's sound speed and its characteristic diameter, offering a new dimension in PARS microscopy. This enables the assessment of the object's elastic properties, deduced from its speed of sound. Additionally, it offers the potential for sizing objects with known sound speeds. The proof of principle experiments was conducted using spherical polystyrene absorbers, ranging in size from 1 to 10 micrometers with known properties, embedded in a Polydimethylsiloxane (PDMS) matrix. This technique expands the scope of PARS imaging, opening new perspectives for clinical applications in mechanobiology by demonstrating its potential for mechanical imaging.

  PublisherOA PDFDOI

• Visual stimulus-evoked transient blood flow and blood vessel diameter changes in the healthy human retina measured with a combined OCT+ERG system

  Biomedical Optics Express · 2025-08-29 · 1 citations

  articleOpen access

  Neurodegenerative retinal diseases, such as glaucoma, age-related macular degeneration and diabetic retinopathy, cause gradual damage to the retinal morphology, blood vasculature, and neuronal function, and ultimately lead to blindness. In this study, a retinal OCT system was combined with a clinical electroretinography (ERG) system to investigate visually-evoked transient changes in the retinal blood flow (RBF) and blood vessel diameter (BVD) in the healthy human retina. The OCT system offered 2.7 µ m axial resolution in retinal tissue and 98 dB sensitivity for 1.1 mW imaging power and 250 kHz image acquisition rate. Doppler OCT (double circular scans around the optic nerve head) and ERG traces were acquired from healthy subjects in response to 10 Hz, white light flicker stimuli and different stimulus intensities. The ERG system was used to generate visual stimuli of precise timing, duration, luminance, and flicker frequency, as well as to confirm the retinal neuronal response to the visual stimulation. MATLAB-based custom algorithms were developed to track time-dependent changes in the RBF and BVD from the OCT images. Results from this study revealed a rapid transient increase in the RBF accompanied by transient vasoconstriction and vasodilation of the retinal blood vessels in response to the flicker stimulation. The amplitude and latency of the RBF and BVD responses were dependent on the stimulus intensity as well as the blood vessel type (arteries or veins).

  PublisherDOI

• Visual stimulus-evoked transient blood flow and blood vessel diameter changes in the healthy human retina measured with a combined OCT+ERG system

  2025-05-05

  preprintOpen access

  Neurodegenerative retinal diseases, such as glaucoma, age-related macular degeneration, and diabetic retinopathy, cause gradual damage to the retinal morphology, blood vasculature and neuronal function, and ultimately lead to blindness. In this study, a retinal OCT system was combined with a clinical electroretinography (ERG) system to investigate visually-evoked transient changes in the retinal blood flow (RBF) and blood vessel diameter (BVD) in the healthy human retina. The OCT system offered 2.7 𝜇m axial resolution in retinal tissue and 98 dB sensitivity for 1.1 mW imaging power and 250 kHz image acquisition rate. Doppler OCT (circular scans around the optic nerve head) and ERG traces were acquired from healthy subjects in response to 10 Hz white light flicker stimuli and different stimulus intensities. MATLAB-based custom algorithms were developed for tracking time-dependent changes in the RBF and BVD from the OCT images. Results from this study revealed a rapid transient increase in the RBF accompanied by transient vasoconstriction and vasodilation of the retinal blood vessels in response to the flicker stimulation. The amplitude and latency of the RBF and BVD responses was dependent on the stimulus intensity as well as the blood vessel type (arteries or veins).

  PublisherOA PDFDOI

Recent grants

• Broadcast-echo recognition for clutter rejection in bat sonar

  NSF · $448k · 2009–2013

• NIH Grant R01DC000511

  NIH · $293k · 1992

• NIH Grant R01MH069633

  NIH · $1.7M · 2009

• NIH Grant T32MH019118

  NIH · $2.5M · 2014

• NIH Grant K02MH000521

  NIH · $741k · 1995

Frequent coauthors

• Andrea Megela Simmons

  Providence College

  256 shared

• Michael J. Ferragamo

  79 shared

• Mary Ellen Bates

  75 shared

• Cynthia F. Moss

  72 shared

• Jason E. Gaudette

  RTX (United States)

  70 shared

• Laura N. Kloepper

  University of New Hampshire

  62 shared

• Chen Ming

  Sichuan University

  61 shared

• Caroline M. DeLong

  Rochester Institute of Technology

  59 shared