Jose Manuel Alonso, M.D., Ph.D.

Distinguished Professor
Visual Neuroscience Laboratory

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Image: Dr. Jose Manuel Alonso at the State University of New York, College of Optometry | Image Credit: SUNY, College of Optometry
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Research & Professional Profile

The Visual World & The Brain

Vision is the brain’s primary way of understanding the world. Every moment, the eyes capture vast amounts of visual information, which the brain must quickly organize and interpret to guide perception and behavior. To accomplish this, the brain breaks each image into fundamental components—much like written language is parsed into letters and words to understand a sentence.The Alonso Laboratory studies the neural circuits that make this process possible. Our research focuses on how visual signals entering the eye are transformed into meaningful representations in the brain and how disruptions in these circuits contribute to visual disorders such as myopia (nearsightedness), amblyopia, and glaucoma.A major focus of our work is understanding two fundamental visual pathways known as ON and OFF pathways, which respond to increases and decreases in light. These pathways originate at the very first synapse of the visual system and are found in all animals capable of forming images, from flies to humans. The Alonso Laboratory has made important contributions to understanding how these pathways are organized and how they work together to extract visual information. Our research has shown that ON and OFF pathways remain largely separate as visual signals travel through the brain, yet they can also converge within individual neurons to create powerful edge-detecting mechanisms that allow the brain to recognize complex shapes and objects—even from a few simple lines.We have also demonstrated that the two pathways respond differently to visual stimuli. ON pathways are particularly sensitive to bright stimuli, large surfaces, low contrast, and slow motion, conditions that are common in natural outdoor environments. These properties make ON pathways highly effective for processing the visual world during normal movement through bright environments.However, these same characteristics may make ON pathways vulnerable to reduced stimulation during prolonged indoor viewing under dim or visually restricted conditions. Recent research from the Alonso Laboratory suggests that insufficient stimulation of ON pathways may increase the risk of developing myopia, a condition that causes blurred distance vision and is rapidly becoming a global epidemic.

Professional Profile

Dr. Alonso is a Distinguished Professor at SUNY College of Optometry whose research bridges visual neuroscience and myopia. His work has been continuously funded by the NIH since 1999, and he has served on the National Advisory Eye Council (NIH/NEI) and chaired NIH study sections.

Education

MD, Universidad de Santiago de Compostela, Spain
MS, Universidad de Santiago de Compostela, Spain
PhD, Neuroscience, Universidad Autónoma de Madrid, Spain
Post Doctoral Fellow, Torsten Wiesel Lab (Nobel Laureate, 1981), Rockefeller University, US

Positions

Distinguished Professor, Biological Sciences, State University of New York, 2014 - present
Professor, Biological Sciences, State University of New York, 2007-2014
Associate Professor, Biological Sciences, State University of New York, 2002-2007
Assistant Professor, Psychology, University of Connecticut, 1999-2002
Research Associate, Laboratory of Neurobiology, Rockefeller University, 1995-1999

Leadership & National Service

Member, National Advisory Eye Council (NAEC), National Eye Institute (NIH), 2018–2022
- Advised on national research priorities and funding strategy in vision science
Chair & Member, NIH Study Sections
- Led and participated in peer review of federally funded research proposals
Reviewing Editor, Journal of Neuroscience
- Oversaw peer review and editorial decisions in systems and visual neuroscience

Research Support & Funding

National Eye Institute (NEI) of the National Institutes of Health (NIH) — Continuous funding as Principal Investigator, 1999–present
Additional support: National Science Foundation (NSF), SUNY Optometry and The University of Connecticut

Selected Honors & Fellowships

SUNY Chancellor Award for Excellence in Scholarship
SUNY Chancellor Award for Research Excellence
Revson Fellowship
Fulbright Fellowship
Fellowship from National Science Foundation, Spain

Selected Publications

Maharjan, U, Rahimi-Nasrabadi, H, Poudel, S, Olianezhad, F, Jin, J, Dul, MW, Alonso, JM. Human accommodative visuomotor function is driven by contrast through ON and OFF pathways and is enhanced in myopia. Cell Reports (2026)
Poudel S, Jin J, Rahimi-Nasrabadi H, Dellostritto S, Dul MW, Viswanathan S and Alonso JM. Contrast sensitivity of ON and OFF human retinal pathways in myopia. Journal of Neuroscience (2024)
Najafian S, Koch E, Teh KL, Jin J, Rahimi-Nasrabadi H, Zaidi Q, Kremkow J, Alonso JM. A theory of cortical map formation in the visual brain. Nature Communications (2022)
Kremkow J, Jin J, Wang Y, Alonso JM. Principles underlying sensory map topography in primary visual cortex. Nature (2016)
Jin J, Wang Y, Swadlow HA, Alonso JM. Population receptive fields of ON and OFF thalamic inputs to an orientation column in visual cortex. Nature Neuroscience (2011)
Alonso JM, Usrey WM, Reid RC. Precisely correlated firing in cells of the lateral geniculate nucleus. Nature (1996)
Reid RC, Alonso JM. Specificity of monosynaptic connections from thalamus to visual cortex. Nature (1995)

Our Team

Jose Manuel Alonso, M.D., Ph.D

Head of Lab

Manoj Mahat

Current Graduate Student

Jin Jianzhong

Research Scientist

Emmanuel Eguae

Current Graduate Student

Urusha Maharjan

Current Graduate Student

Stephen Dellostritto, OD, MS, FAAO

Current Graduate Student

Farzaneh Olianezhad

Current Graduate Student

Collaborators

Mitchell W. Dul, OD

Professor

SUNY Optometry

Xiaoying Zhu, Ph.D.

Associate Clinical Professor

SUNY Optometry

Stephen Dellostritto, OD, MS, FAAO

Assistant Clinical Professor

SUNY Optometry

Alexandra Benavente-Perez, Ph.D.

Associate Clinical Professor

SUNY Optometry

Qasim Zaidi, Ph.D.

Distinguished Professor

SUNY Optometry

Harvey Swadlow, Ph.D.

Professor

University of Connecticut

Jingyun Wang, Ph.D.

Associate Professor

SUNY Optometry

Yulia Bereshpolova, Ph.D.

Assistant Research Professor

University of Connecticut

Alumni

Post Doctoral Fellows

Adam Tengolics, Ph.D.

Postdoctoral Fellow

Icahn School of Medicine

Xiaobing Li, Ph.D.

Assistant Professor

University of Alabama

Luis M. Martinez, Ph.D.

Research Scientist

Neuroscience Institute, Alicante

Darlene Archer, Ph.D.

Postdoctoral Fellow

New York University

Yao Chen, Ph.D.

Professor

Shanghai Jiao Tong University

Reeze Mazade, Ph.D.

Research Scientist

Georgia Institute of Technology

Monica Cano Vinas, Ph.D.

Current Position Unknown

Jens Kremkow, Ph.D.

Assistant Professor

University of Berlin

Jianzhong Jin, Ph.D.

Research Scientist

SUNY Optometry

Graduate Students

Sohrab Najafian, Ph.D.

Postdoctoral Fellow

Harvard Medical School

Lauren Wool, Ph.D.

Data Scientist

Greater London Authority

Sanjiv Anand, M.D.

Nephrologist

Sabina Poudel, Ph.D.

Postdoctoral Fellow

University of Rochester

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Hamed Rahimi, Ph.D.

Postdoctoral Fellow

Rockefeller University

Mike Jansen, Ph.D.

Current Position Unknown

Yushi Wang, Ph.D.

Current Position Unknown

Carmen Pons, M.D., Ph.D.

Neurosurgery Resident

University of Chicago Medical School

Stanley Komban, Ph.D.

Research Scientist

Meltwater

Chong Weng, Ph.D.

Director & Actuary

Prudential Financial

Erin Koch, Ph.D.

Senior Data Scientist

Kernel

Reza Lashgari, Ph.D.

Research Scientist

Shahid Beheshti University

Chun-I Yeh, Ph.D.

Assistant Professor

National University of Taiwan

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Research Publications

Graphical excerpt from Jose Manuel Alonso research paper

Maharjan, U., Rahimi-Nasrabadi, H., Poudel, S., Olianezhad, F., Jin, J., Dul, M., Alonso, J.M. (2026) Human accommodative visuomotor function is driven by contrast through ON and OFF pathways and is enhanced in myopia. Cell Reports DOI: 10.1016/j.celrep.2026.116938
Olianezhad, F., Jianzhong, J., Najafian, S., Maruya, A., Zaidi, Q., Alonso, J.M. (2025). Visual Distortions in Human Amblyopia Are Correlated with Deficits in Contrast Sensitivity. Journal of Neuroscience DOI: 10.1523/JNEUROSCI.1111-25.2025
Pons, C, Mazade, R. , Jin, J, Dul, M., Alonso, JM. (2025). Optical defocus affects differently ON and OFF visual pathways. iScience https:/cell.com/iscience/fulltext/S2589-0042
Su, C., Mendes-Platt, R.F., Alonso, J.M., Swadlow, H.A ., Bereshpolova, Y. (2025). Fast-spike interneurons in visual cortical layer 5: Heterogeneous response properties are related to thalamocortical connectivity. Journal of Neuroscience https://doi.org/10.1523/JNEUROSCI.1116-24.
Olianezhad, F., Jin, J., Najafian, S., Pons, C., Mazade, R., Kremkow, J., Alonso, J.M. (2024). Binocular receptive-field construction in the primary visual cortex. Current Biology 34 (11), 2474-2486. e5.
Su, C., Mendes-Platt, R.F., Alonso, J.M., Swadlow, H.A ., Bereshpolova, Y. (2024). Retinal direction of motion is reliably transmitted to visual cortex through highly selective thalamocortical connections. Current Biology doi: 10.1016/j.cub.2024.11.013.
Su, C., Mendes-Platt, R.F., Alonso, J.M., Swadlow, H.A ., Bereshpolova, Y. (2024). Visual corticotectal neurons in awake rabbits: Receptive fields and driving monosynaptic thalamocortical inputs. Journal of Neuroscience 44(19): 3, 1-14.
Poudel, S., Jin, J., Rahimi-Nasrabadi, H., Dellostritto, S., Dul, M.W., Viswanathan, S., Alonso, J.M. (2024). Contrast Sensitivity of ON and OFF Human Retinal Pathways in Myopia. Journal of Neuroscience 44(3): e1487232023.
Poudel, S., Rahimi-Nasrabadi, H., Jin, J., Najafian, S., Alonso, J.M. (2023). Differences in visual stimulation between reading and walking, and implications for myopia development. Journal of Vision 23(4): 3, 1-26.
Rahimi-Nasrabadi, H., V. Moore-Stoll, J. Tan, S. Dellostritto, J. Jin, M. W. Dul and J. M. Alonso (2023). Luminance Contrast Shifts Dominance Balance between ON and OFF Pathways in Human Vision. Journal of Neuroscience 43(6): 993-1007.
Mazade, R., J. Jin, H. Rahimi-Nasrabadi, S. Najafian, C. Pons and J. M. Alonso (2022). Cortical mechanisms of visual brightness. Cell Reports 40(13): 111438.
Najafian, S., E. Koch, K. L. Teh, J. Jin, H. Rahimi-Nasrabadi, Q. Zaidi, J. Kremkow and J. M. Alonso (2022). A theory of cortical map formation in the visual brain. Nature Communications 13(1): 2303.
Rahimi-Nasrabadi and J. M. Alonso (2022) Modular Streaming Pipeline of Eye/Head Tracking Data Using Tobii Pro Glasses 3 bioRxiv, (2022)
Alonso, J.M., Scanziani, S. (2022), Thalamocortical interactions in the primary visual cortex. Chapter 9. The thalamus. Edited by Michale M. Halassa. Cambridge University Press
Kremkow, J., and Alonso, J. M. (2021). Functional specificity of afferent connections in visual thalamus. Neuron 109, 2368-2370.
Rahimi-Nasrabadi, H., et al. (2021). Image luminance changes contrast sensitivity in visual cortex. Cell Reports 34(5): 108692.
Bereshpolova, Y., et al. (2020), Three rules govern thalamocortical connectivity of fast-spike inhibitory interneurons in the visual cortex. eLife.
Mazade, R. and J. M. Alonso (2019), Synergy in Cortical Networks. Neuron 104 (2), 184-185.
Bereshpolova, Y., C. R. Stoelzel, C. Su, J. M. Alonso and H. A. Swadlow (2019). Activation of a Visual Cortical Column by a Directionally Selective Thalamocortical Neuron.Cell Reports 27(13): 3733-3740 e3.
Jansen, M., J. Jin, X. Li, R. Lashgari, J. Kremkow, Y. Bereshpolova, H. A. Swadlow, Q. Zaidi and J. M. Alonso, (2019), Cortical Balance Between ON and OFF Visual Responses Is Modulated by the Spatial Properties of the Visual Stimulus. Cerebral Cortex 29(1): 336-355.
Macknik SL, RG Alexander, O Caballero, J Chanovas, KJ Nielsen, N Nishimura, CB Schaffer, H Slovin, A Babayoff, R Barak, S Tang, N Ju, A Yazdan-Shahmorad, JM Alonso, E Malinskiy, S Martinez-Conde (2019), Advanced Circuit and Cellular Imaging Methods in Nonhuman Primates. Journal of Neuroscience 39 (42), 8267-8274.
Mazade, R., J. Jin, C. Pons and J. M. Alonso (2019). Functional Specialization of ON and OFF Cortical Pathways for Global-Slow and Local-Fast Vision. Cell Reports 27(10): 2881-2894 e5.
Najafian S, J Jin, JM Alonso (2019) Diversity of ocular dominance patterns in visual cortex originates from variations in local cortical retinotopy. Journal of Neuroscience 39 (46), 9145-9163.
Pons, C., J. Jin, R. Mazade, M. Dul, Q. Zaidi and J. M. Alonso (2019). Amblyopia Affects the ON Visual Pathway More than the OFF. Journal of Neuroscience 39(32): 6276-6290.
Alonso, J.M. (2018). Motion processing picks up speed in the brain. Nature 558(7708): 38-39.
Mazade R, Niell CM, Alonso JM (2018) Seeing with a biased visual cortical map. Journal of Neurophysiology 120(1): 272-273.
Kremkow, J., Alonso, J.M. (2018). Thalamocortical circuits and functional architecture. Annual Review of Visual Sciences 4: 263-285.
Luo-Li, G. Mazade, R. , Zaidi, Q., Alonso, J.M., Freeman A. (2018). Motion changes response balance between ON and OFF visual pathways. Communications Biology 1 (60):1-5.
Pons, C., Mazade, R., Jin, J., Dul, M.W., Zaidi, Q., Alonso, J.M. (2017) Neuronal mechanisms underlying differences in spatial resolution between darks and lights in human vision. Journal of Vision 17(14): 5.
Mazade R. and J. M. Alonso (2017) Thalamocortical processing in vision. (invited review) Visual Neuroscience 34 (e007):1-9.
Swadlow, H. A. and J. M. Alonso (2017). Multielectrodes join the connectome. Nature Methods 14(9): 847-848.
Stoelzel, C. R., Y. Bereshpolova, J. M. Alonso and H. A. Swadlow (2017). Axonal Conduction Delays, Brain State, and Corticogeniculate Communication. The Journal of Neuroscience 37(26): 6342-6358.
Hagen, E., J. C. Fossum, K. H. Pettersen, J. M. Alonso, H. A. Swadlow and G. T. Einevoll (2017). Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection. The Journal of Neuroscience 37(20): 5123-5143.
Alonso, J. M. (2016). The Geometry of Visual Cortical Maps. Neuron 91(4): 716-718.
Koch, E., J. Jin, J. M. Alonso and Q. Zaidi (2016). Functional implications of orientation maps in primary visual cortex. Nature Communications 7: 13529.
Kremkow, J., J. Jin, Y. Wang and J. M. Alonso (2016). Principles underlying sensory map topography in primary visual cortex. Nature 533(7601): 52-57.
Kremkow, J., L. U. Perrinet, C. Monier, J. M. Alonso, A. Aertsen, Y. Fregnac and G. S. Masson (2016). Push-Pull Receptive Field Organization and Synaptic Depression: Mechanisms for Reliably Encoding Naturalistic Stimuli in V1. Frontiers in Neural Circuits 10: 37.
Alonso, J. M. and H. A. Swadlow (2015). Thalamus controls recurrent cortical dynamics. Nature Neuroscience 18(12): 1703-4.
Zhao, L., C. Sendek, V. Davoodnia, R. Lashgari, M. W. Dul, Q. Zaidi and J. M. Alonso (2015). Effect of Age and Glaucoma on the Detection of Darks and Lights. Investigative Ophthalmology & Visual Science 56(11): 7000-6.
Stoelzel, C. R., J. M. Huff, Y. Bereshpolova, J. Zhuang, X. Hei, J. M. Alonso and H. A. Swadlow (2015). Hourlong adaptation in the awake early visual system. Journal of Neurophysiology: jn 00116 2015.
Wang, Y., J. Jin, J. Kremkow, R. Lashgari, S. J. Komban and J. M. Alonso (2015). Columnar organization of spatial phase in visual cortex. Nature Neuroscience 18(1): 97-103.
Hei, X., C. R. Stoelzel, J. Zhuang, Y. Bereshpolova, J. M. Huff, J. M. Alonso and H. A. Swadlow (2014). Directional selective neurons in the awake LGN: Response properties and modulation by brain state. Journal of Neurophysiology.
Kelly, S. T., J. Kremkow, J. Jin, Y. Wang, Q. Wang, J. M. Alonso and G. B. Stanley (2014). The role of thalamic population synchrony in the emergence of cortical feature selectivity. PLoS Computational Biology 10(1): e1003418.
Komban, S. J., J. Kremkow, J. Jin, Y. Wang, R. Lashgari, X. Li, Q. Zaidi and J. M. Alonso (2014). Neuronal and perceptual differences in the temporal processing of darks and lights. Neuron 82(1): 224-34.
Kremkow, J., J. Jin, S. J. Komban, Y. Wang, R. Lashgari, X. Li, M. Jansen, Q. Zaidi and J. M. Alonso (2014). Neuronal nonlinearity explains greater visual spatial resolution for darks than lights. Proceedings of the National Academy of Sciences of the United States of America 111(8): 3170-5.
Jansen, M., X. Li, R. Lashgari, J. Kremkow, Y. Bereshpolova, H. A. Swadlow, Q. Zaidi and J. M. Alonso (2014). Chromatic and Achromatic Spatial Resolution of Local Field Potentials in Awake Cortex. Cerebral Cortex: 10.1093/cercor/bhu270.
Li, X., Y. Chen, R. Lashgari, Y. Bereshpolova, H. A. Swadlow, B. B. Lee and J. M. Alonso (2014). Mixing of Chromatic and Luminance Retinal Signals in Primate Area V1. Cerebral Cortex: 10.1093/cercor/bhu002
Sean T. Kelly, J. Kremkow, J. Jin, Y. Wang, Q. Wang, J.M. Alonso, Stanley, G. B (2014). The role of thalamic population synchrony in the emergence of cortical feature selectivity. PLoS Computational Biology 10(1): e1003418.
Swadlow, H.A. and Alonso, J.M. (2014) Brain state and geniculocortical communication. The New Visual Neurosciences. Edited by J.S. Werner and L.M. Chalupa. MIT press.
Zhuang, J., Bereshpolova, C. R. Stoelzel, Y., J. M. Huff, X. Hei, J. M. Alonso and H. A. Swadlow (2014). Brain state effect on layer 4 of the awake visual cortex. The Journal of Neuroscience 34(11): 3888-900.
Zhuang, J., C. R. Stoelzel, Y. Bereshpolova, J. M. Huff, X. Hei, J. M. Alonso and H. A. Swadlow (2013). Layer 4 in primary visual cortex of the awake rabbit: contrasting properties of simple cells and putative feedforward inhibitory interneurons. The Journal of Neuroscience 33(28): 11372-89.
Lashgari, R., X. Li, Y. Chen, J. Kremkow, Y. Bereshpolova, H. A. Swadlow and J. M. Alonso (2012). Response properties of local field potentials and neighboring single neurons in awake primary visual cortex. The Journal of Neuroscience 32(33): 11396-413.
Stanley, G. B., J. Jin, Y. Wang, G. Desbordes, Q. Wang, M. J. Black and J. M. Alonso (2012). Visual Orientation and Directional Selectivity through Thalamic Synchrony. The Journal of Neuroscience 32(26): 9073-88.
Butts, D. A., C. Weng, J. Jin, J. M. Alonso and L. Paninski (2011). Temporal precision in the visual pathway through the interplay of excitation and stimulus-driven suppression. The Journal of Neuroscience 31(31): 11313-27.
Bereshpolova, Y., C. R. Stoelzel, J. Zhuang, Y. Amitai, J. M. Alonso and H. A. Swadlow (2011). Getting drowsy? Alert/nonalert transitions and visual thalamocortical network dynamics. The Journal of Neuroscience 31(48): 17480-7.
Jin, J., Y. Wang, R. Lashgari, H. A. Swadlow and J. M. Alonso (2011). Faster thalamocortical processing for dark than light visual targets. The Journal of Neuroscience 31(48): 17471-9.
Jin, J., Y. Wang, H. A. Swadlow and J. M. Alonso (2011). Population receptive fields of ON and OFF thalamic inputs to an orientation column in visual cortex. Nature Neuroscience 14(2): 232-8. News and Views associated to this paper: Ringach, D. L. (2011). You get what you get and you don't get upset. Nature Neuroscience 14(2): 123-4.
Komban, S. J., J. M. Alonso and Q. Zaidi (2011). Darks are processed faster than lights. The Journal of Neuroscience 31(23): 8654-8.
Butts, D. A., G. Desbordes, C. Weng, J. Jin, J. M. Alonso and G. B. Stanley (2010). The episodic nature of spike trains in the early visual pathway. Journal of Neurophysiology 104(6): 3371-87.
Desbordes, G., J. Jin, J. M. Alonso and G. B. Stanley (2010). Modulation of temporal precision in thalamic population responses to natural visual stimuli. Frontiers in Systems Neuroscience 4: 151.
Chen, Y., S. Anand, S. Martinez-Conde, S. L. Macknik, Y. Bereshpolova, H. A. Swadlow and J. M. Alonso (2009). The linearity and selectivity of neuronal responses in awake visual cortex. Journal of Vision 9(9): 12 1-17.
Alonso, J. M. (2009). My recollections of Hubel and Wiesel and a brief review of functional circuitry in the visual pathway. Journal of Physiology 587(Pt 12): 2783-90.
Yeh, C. I., C. R. Stoelzel, C. Weng and J. M. Alonso (2009). Functional consequences of neuronal divergence within the retinogeniculate pathway. Journal of Neurophysiology 101(4): 2166-85.
Swadlow, H. A. and J. M. Alonso (2009). Spikes are making waves in the visual cortex. Nature Neuroscience 12(1): 10-1.
Alonso, J. M., C. I. Yeh and C. R. Stoelzel (2008). Visual stimuli modulate precise synchronous firing within the thalamus. Thalamus & Related Systems 4(1): 21-34.
Desbordes, G., J. Jin, C. Weng, N. A. Lesica, G. B. Stanley and J. M. Alonso (2008). Timing precision in population coding of natural scenes in the early visual system. PLoS Biology 6(12): e324.