Daniel Benjamin Aharoni
Assistant Professor-in-Residence, Neurology, University of California Los Angeles
Our 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.
Publications
- Guo C, Blair GJ, Sehgal M, Sangiuliano Jimka FN, Bellafard A, Silva AJ, Golshani P, Basso MA, Blair HT, Aharoni D. Miniscope-LFOV: A large-field-of-view, single-cell-resolution, miniature microscope for wired and wire-free imaging of neural dynamics in freely behaving animals.. Science advances, 2023.
- Chen Z, Blair GJ, Cao C, Zhou J, Aharoni D, Golshani P, Blair HT, Cong J. FPGA-Based In-Vivo Calcium Image Decoding for Closed-Loop Feedback Applications.. IEEE transactions on biomedical circuits and systems, 2023.
- Hur SW, Safaryan K, Yang L, Blair HT, Masmanidis SC, Mathews PJ, Aharoni D, Golshani P. Correlated signatures of social behavior in cerebellum and anterior cingulate cortex.. bioRxiv : the preprint server for biology, 2023.
- Chen Z, Blair GJ, Guo C, Zhou J, Romero-Sosa JL, Izquierdo A, Golshani P, Cong J, Aharoni D, Blair HT. A hardware system for real-time decoding of in vivo calcium imaging data.. eLife, 2023.
- Gabriel CJ, Zeidler Z, Jin B, Guo C, Goodpaster CM, Kashay AQ, Wu A, Delaney M, Cheung J, DiFazio LE, Sharpe MJ, Aharoni D, Wilke SA, DeNardo LA. BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking.. eLife, 2022.
- Shuman T, Aharoni D, Cai DJ, Lee CR, Chavlis S, Page-Harley L, Vetere LM, Feng Y, Yang CY, Mollinedo-Gajate I, Chen L, Pennington ZT, Taxidis J, Flores SE, Cheng K, Javaherian M, Kaba CC, Rao N, La-Vu M, Pandi I, Shtrahman M, Bakhurin KI, Masmanidis SC, Khakh BS, Poirazi P, Silva AJ, Golshani P. Breakdown of spatial coding and interneuron synchronization in epileptic mice.. Nature neuroscience, 2020.
- Aharoni D, Hoogland TM. Circuit Investigations With Open-Source Miniaturized Microscopes: Past, Present and Future.. Frontiers in cellular neuroscience, 2019.
- Aharoni D, Khakh BS, Silva AJ, Golshani P. All the light that we can see: a new era in miniaturized microscopy.. Nature methods, 2019.
- Skocek O, Nöbauer T, Weilguny L, Traub FM, Xia CN, Molodtsov MI, Grama A, Yamagata M, Aharoni D, Cox DD, Golshani P, Vaziri A. Author Correction: High-speed volumetric imaging of neuronal activity in freely moving rodents.. Nature methods, 2018.
- Skocek O, Nöbauer T, Weilguny L, Martínez Traub F, Xia CN, Molodtsov MI, Grama A, Yamagata M, Aharoni D, Cox DD, Golshani P, Vaziri A. High-speed volumetric imaging of neuronal activity in freely moving rodents.. Nature methods, 2018.
- Cai DJ, Aharoni D, Shuman T, Shobe J, Biane J, Song W, Wei B, Veshkini M, La-Vu M, Lou J, Flores SE, Kim I, Sano Y, Zhou M, Baumgaertel K, Lavi A, Kamata M, Tuszynski M, Mayford M, Golshani P, Silva AJ. A shared neural ensemble links distinct contextual memories encoded close in time.. Nature, 2016.
- Shtrahman M, Aharoni DB, Hardy NF, Buonomano DV, Arisaka K, Otis TS. Multifocal fluorescence microscope for fast optical recordings of neuronal action potentials.. Biophysical journal, 2015.
- Cushman JD, Aharoni DB, Willers B, Ravassard P, Kees A, Vuong C, Popeney B, Arisaka K, Mehta MR. Multisensory control of multimodal behavior: do the legs know what the tongue is doing?. PloS one, 2013.
- Michalet X, Colyer RA, Scalia G, Kim T, Levi M, Aharoni D, Cheng A, Guerrieri F, Arisaka K, Millaud J, 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.