Daniel Aharoni

A Short Biography:

My research lies at the intersection of engineering, neuroscience, and physics. In particular, we focus on applying tool development methodologies from engineering and physics to address current challenges in neuroscience and medicine. Working often times in close collaboration with other researchers, we concentrate on finding solutions to critical design problems (hardware, software, analysis, experimental) and develop those solutions from concept to implementation. In recent years, Dr. Aharoni led the development of the Miniscope system, an open-source microscopy platform for recording and analyzing neural activity in freely behaving animals. Our platform is currently being used in over 450 laboratories with an active and growing user base, making it one of the most successful open-source neuroscience tools to date.

Our work is motivated by two goals: (i) to contribute to the growing trend of democratizing access to transformative tools in neuroscience, and (ii) to bridge the gap between specialized tool design and the intricacies of modern neuroscience. Specifically, the lab’s research program focuses on expanding optical, electrical, and behavioral techniques through the development of novel, yet accessible, tools that generate quantitatively and qualitatively new types of data.

Work Titles
UCLA Assistant Professor, David Geffen School of Medicine at UCLA

Contact Information:

Work Phone Number:


Mailing Address:

B2-414 MDCC
Los Angeles, CA 90095


A selected list of publications:

Shuman Tristan, Aharoni Daniel, Cai Denise J, Lee Christopher R, Chavlis Spyridon, Page-Harley Lucia, Vetere Lauren M, Feng Yu, Yang Chen Yi, Mollinedo-Gajate Irene, Chen Lingxuan, Pennington Zachary T, Taxidis Jiannis, Flores Sergio E, Cheng Kevin, Javaherian Milad, Kaba Christina C, Rao Naina, La-Vu Mimi, Pandi Ioanna, Shtrahman Matthew, Bakhurin Konstantin I, Masmanidis Sotiris C, Khakh Baljit S, Poirazi Panayiota, Silva Alcino J, Golshani Peyman   Breakdown of spatial coding and interneuron synchronization in epileptic mice Nature neuroscience, 2020; 23(2): 229-238.
Aharoni Daniel, Khakh Baljit S, Silva Alcino J, Golshani Peyman   All the light that we can see: a new era in miniaturized microscopy Nature methods, 2019; 16(1): 11-13.
Aharoni Daniel, Hoogland Tycho M   Circuit Investigations With Open-Source Miniaturized Microscopes: Past, Present and Future Frontiers in cellular neuroscience, 2019; 13(2): 141.
Skocek Oliver, Nöbauer Tobias, Weilguny Lukas, Martínez Traub Francisca, Xia Chuying Naomi, Molodtsov Maxim I, Grama Abhinav, Yamagata Masahito, Aharoni Daniel, Cox David D, Golshani Peyman, Vaziri Alipasha   High-speed volumetric imaging of neuronal activity in freely moving rodents Nature methods, 2018; 15(6): 429-432.
Cai Denise J, Aharoni Daniel, Shuman Tristan, Shobe Justin, Biane Jeremy, Song Weilin, Wei Brandon, Veshkini Michael, La-Vu Mimi, Lou Jerry, Flores Sergio E, Kim Isaac, Sano Yoshitake, Zhou Miou, Baumgaertel Karsten, Lavi Ayal, Kamata Masakazu, Tuszynski Mark, Mayford Mark, Golshani Peyman, Silva Alcino J   A shared neural ensemble links distinct contextual memories encoded close in time Nature, 2016; 534(7605): 115-8.
Shtrahman Matthew, Aharoni Daniel B, Hardy Nicholas F, Buonomano Dean V, Arisaka Katsushi, Otis Thomas S   Multifocal fluorescence microscope for fast optical recordings of neuronal action potentials Biophysical journal, 2015; 108(3): 520-9.
Ravassard Pascal, Kees Ashley, Willers Bernard, Ho David, Aharoni Daniel A, Cushman Jesse, Aghajan Zahra M, Mehta Mayank R   Multisensory control of hippocampal spatiotemporal selectivity Science (New York, N.Y.), 2013; 340(6138): 1342-1346.
Cushman Jesse D, Aharoni Daniel B, Willers Bernard, Ravassard Pascal, Kees Ashley, Vuong Cliff, Popeney Briana, Arisaka Katsushi, Mehta Mayank R   Multisensory control of multimodal behavior: do the legs know what the tongue is doing? PloS one, 2013; 8(11): e80465.
Michalet X, Colyer R A, Scalia G, Kim T, Levi Moran, Aharoni Daniel, Cheng Adrian, Guerrieri F, Arisaka Katsushi, Millaud Jacques, Rech I, Resnati D, Marangoni S, Gulinatti A, Ghioni M, Tisa S, Zappa F, Cova S, Weiss S   High-throughput single-molecule fluorescence spectroscopy using parallel detection Proceedings of SPIE--the International Society for Optical Engineering, 2010; 7608(76082D): 1342-1346.

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