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

Distinguished Professor
Visual Neuroscience Laboratory

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The Visual World & The Brain

Research Overview

The brain is a fascinating structure that has evolved over 500+ million years to explore and interact with the environment. Brains capture information through the senses and, in humans, vision dominates sensory perception. To comprehend what we see, our brain parses each image into basic building blocks just as it parses sentences into words and letters to comprehend text. The Alonso laboratory investigates the brain circuits involved in this image parsing process, and their role in visual disorders such as myopia, amblyopia and glaucoma. The laboratory has made major contributions towards understanding the organization and function of two main brain pathways involved in processing light and dark stimuli. These two pathways, called ON and OFF because they respond to light-on or light-off, play a crucial role in vision. They originate in the eye at the very first synapse of the visual system and are present in all species that can form images, from flies to humans.

The Alonso laboratory demonstrated that ON and OFF pathways remain functionally segregated throughout the visual system, but can also converge in the same brain cell and work together. The functional segregation explains why humans do not become blind when genetic mutations inactivate ON pathways. The convergence (ON-OFF edge detectors) explain why humans only require a few lines to accurately identify stimuli such as face sketches. The Alonso laboratory also demonstrated that ON and OFF pathways have different stimulus preferences, with ON pathways responding better to bright stimuli, large surfaces, low contrasts, and slow motion. These preferences are ideal to extract information from a bright visual world that is slowly drifting with self-motion, but also make ON pathways vulnerable to stationary vision in poorly-illuminated environments. Recent work from the Alonso laboratory also indicates that poor stimulation of ON pathways increases the risk of developing myopia (nearsightedness), a visual disorder that blurs vision at far distance and is becoming a global epidemic.

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, 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

Awards & Honors

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

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)
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)
Kremkow J, Jin J, Wang Y, Alonso JM. Principles underlying sensory map topography in primary visual cortex. Nature (2016)
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)

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Websites & Social Media

SUNY, College of Optometry Faculty Page
Lab Website: www.alonsolab.org

[email protected]

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Our Team

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

Head of Lab

Urusha Maharjan

Current Graduate Student

Jin Jianzhong

Research Scientist

Sabina Poudel

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

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

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

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.
Jin, J. Z., C. Weng, C. I. Yeh, J. A. Gordon, E. S. Ruthazer, M. P. Stryker, H. A. Swadlow and J. M. Alonso (2008). On and off domains of geniculate afferents in cat primary visual cortex. Nature Neuroscience 11(1): 88-94.
Chen, Y., Martinez-Conde, S., Macknik, S.L., Bereshpolova, Y., Swadlow, H.A., Alonso, J.M. (2008) Task difficulty modulates the activity of specific neuronal populations in primary visual cortex. Nature Neuroscience 11 (8): 975-982.
Butts, D.A., C. Weng, J. Jin, C.I. Yeh, N.A. Lesica, J.M. Alonso and G.B. Stanley (2007) Temporal precision in the neural code and the time scales of natural vision.Nature 449:92-95.
Lesica, N. A., J. Jin, C. Weng, C. I. Yeh, D. A. Butts, G. B. Stanley and J. M. Alonso (2007). Adaptation to Stimulus Contrast and Correlations during Natural Visual Stimulation. Neuron 55(3): 479-91.
Alonso, J. M. (2007). El talamo y la vision. Investigacion y Ciencia 22: 26-32.
Alonso, J. M. (2006). Neurons find strength through synchrony in the brain. Science 312: 1604-05.
Alonso, J. M. (2006). La vía visual cien años después de Ramón y Cajal. Santiago Ramón y Cajal. Cien años después. A. G. y. A. Ferrús. les Illes Balears, Editorial Pirámide - Universitat de les Illes Balears: 233-255.
Alonso, J. M., C. I. Yeh, C. Weng and C. Stoelzel (2006). Chapter 1 Retinogeniculate connections: a balancing act between connection specificity and receptive field diversity. Progress in Brain Research 154: 3-13.
Bezdudnaya, T., M. Cano, Y. Bereshpolova, C. R. Stoelzel, J. M. Alonso and H. A. Swadlow (2006). Thalamic Burst Mode and Inattention in the Awake LGNd. Neuron 49(3): 421-32.
Cano, M., T. Bezdudnaya, H. A. Swadlow and J. M. Alonso (2006). Brain state and contrast sensitivity in the awake visual thalamus. Nature Neuroscience 9(10): 1240-2.
Lesica, N. A., C. Weng, J. Jin, C. I. Yeh, J. M. Alonso and G. B. Stanley (2006). Dynamic Encoding of Natural Luminance Sequences by LGN Bursts. PLoS Biology 4(7): e209.
Veredas FJ, Vico FJ, Alonso JM (2006) [Evolving networks of integrate and fire neurons](https://www.sciencedirect.com/science/article/abs/pii/S0925231205