Publications

* equal contribution · † co-corresponding author. A complete record is on ORCID. For the 200+ papers by other groups that use our tools, see Impact.

Peer-reviewed articles

• MiniFAST: a sensitive and fast miniaturized microscope for neural recording Juneau J, Duret G, Chu JP, Madruga B, Dorian CC, Rodriguez AV, Morozov S, Aharoni D, Robinson JT, St-Pierre F, Golshani P, Kemere C Neurophotonics, 2026 · doi:10.1117/1.NPh.13.S2.S23203
• Open-source, high performance miniature 2-photon microscopy systems for freely behaving animals Madruga BA, Dorian CC, Yang L, Sehgal M, Silva AJ, Shtrahman M, Aharoni D, Golshani P Nature Communications, August 2025 · doi:10.1038/s41467-025-62534-y
• Simultaneous two-color imaging with a dual-channel miniscope in freely behaving mice Dong Z, Feng Y, Diego K, Baggetta AM, Sweis BM, Pennington ZT, Lamsifer SI, Zaki Y, Sangiuliano F, Philipsberg PA, Morales-Rodriguez D, Kircher D, Slesinger P, Shuman T, Aharoni D, Cai DJ Science Advances, July 2025 · doi:10.1126/sciadv.adr6470
• MiniXL: An open-source, large field-of-view epifluorescence miniature microscope for mice capable of single-cell resolution and multi-brain region imaging Zhao P*, Guo C*, Xie M, Chen L, Golshani P, Aharoni D Science Advances, June 2025 · doi:10.1126/sciadv.ads4995
• GRIN lens implantation strategies for in vivo calcium imaging using miniature microscopy Zhao P, Aharoni D, Golshani P PLOS ONE, May 2025 · doi:10.1371/journal.pone.0323256
• Transforming neural activity into generative audio-visual art: an interplay between brain data, music, and visuals Uhm SH, Sangiuliano Jimka F, Aharoni D Emille: Journal of the Korean Electro-Acoustic Music Society, vol. 22, 65–75, December 2024
• Correlated signatures of social behavior in cerebellum and anterior cingulate cortex Hur SW, Safaryan K, Yang L, Blair HT, Masmanidis SC, Mathews PJ, Aharoni D†, Golshani P† eLife, 2024 · doi:10.7554/eLife.88439.3
• Hippocampal place cell remapping occurs with memory storage of aversive experiences Blair GJ, Guo C, Wang S, Fanselow MS, Golshani P, Aharoni D, Blair HT eLife, July 2023 · doi:10.7554/eLife.80661
• FPGA-based in-vivo calcium image decoding for closed-loop feedback applications Chen Z, Blair GJ, Cao C, Zhou J, Aharoni D, Golshani P, Blair HT, Cong J IEEE Transactions on Biomedical Circuits and Systems, 17(2), 169–179, April 2023 · doi:10.1109/TBCAS.2023.3268184
• 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 Guo C*, Blair GJ*, Sehgal M, Sangiuliano Jimka FN, Bellafard A, Silva AJ, Golshani P, Basso MA, Blair HT, Aharoni D Science Advances, April 2023 · doi:10.1126/sciadv.adg3918
• A hardware system for real-time decoding of in vivo calcium imaging data Chen Z, Blair GJ, Guo C, Zhou J, Romero-Sosa JL, Izquierdo A, Golshani P, Cong J, Aharoni D, Blair HT eLife, January 2023 · doi:10.7554/eLife.78344
• BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking 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 eLife, August 2022 · doi:10.7554/eLife.74314
• Minian, an open-source miniscope analysis pipeline Dong Z, Mau W, Feng Y, Pennington ZT, Chen L, Zaki Y, Rajan K, Shuman T, Aharoni D†, Cai DJ† eLife, June 2022 · doi:10.7554/eLife.70661
• Breakdown of spatial coding and interneuron synchronization in epileptic mice 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 Nature Neuroscience, January 2020 · doi:10.1038/s41593-019-0559-0
• High-speed volumetric imaging of neuronal activity in freely moving rodents 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 Nature Methods, May 2018 · doi:10.1038/s41592-018-0008-0
• A shared neural ensemble links distinct contextual memories encoded close in time 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 Nature, 534(7605), May 2016 · doi:10.1038/nature17955
• Multifocal fluorescence microscope for fast optical recordings of neuronal action potentials Shtrahman M, Aharoni D, Hardy NF, Buonomano DV, Arisaka K, Otis TS Biophysical Journal, 108(3), February 2015 · doi:10.1016/j.bpj.2014.12.005
• Multisensory control of multimodal behavior: do the legs know what the tongue is doing? Cushman JD*, Aharoni D*, Willers B, Ravassard P, Kees A, Vuong C, Popeney B, Arisaka K, Mehta MR PLOS ONE, 8(11), November 2013 · doi:10.1371/journal.pone.0080465
• Multisensory control of hippocampal spatiotemporal selectivity Ravassard P*, Kees A*, Willers B*, Ho D, Aharoni D, Cushman JD, Aghajan ZM, Mehta MR Science, 340(6138), May 2013 · doi:10.1126/science.1232655
• Development of new photon-counting detectors for single-molecule fluorescence microscopy Michalet X, Colyer RA, Scalia G, Ingargiola A, Lin R, Millaud JE, Weiss S, Siegmund OHW, Tremsin AS, Vallerga JV, Cheng A, Levi M, Aharoni D, Arisaka K, Villa F, Guerrieri F, Panzeri F, Rech I, Gulinatti A, Zappa F, Ghioni M, Cova S Philosophical Transactions of the Royal Society B, 368(1611), February 2013 · doi:10.1098/rstb.2012.0035
• Characterization of the Quartz Photon Intensifying Detector (QUPID) for noble liquid detectors Teymourian A, Aharoni D, Baudis L, Beltrame P, Brown E, Cline D, Ferella AD, Fukasawa A, Lam CW, Lim T, Meng Y, Muramatsu S, Pantic E, Suyama M, Wang H, Arisaka K Nuclear Instruments and Methods in Physics Research A, 654(1), 2011 · doi:10.1016/j.nima.2011.07.015
• XAX: a multi-ton, multi-target detection system for dark matter, double beta decay, and pp solar neutrinos Arisaka K, Wang H, Smith PF, Cline D, Teymourian A, Brown E, Ooi W, Aharoni D, Lam CW, Lung K, Davies S, Price M Astroparticle Physics, 31(2), 2009 · doi:10.1016/j.astropartphys.2008.11.007

Preprints

• STIMscope: centimeter-scale all-optical imaging and patterned optogenetic manipulation at single-cell resolution Chorsi H, Soldado-Magraner S, Jin Y, Soltanalipouryekesammak I, Zheng A, Markovic D, Geschwind DH, Golshani P, Buonomano DV, Aharoni D bioRxiv, May 2026 · doi:10.64898/2026.05.27.728160

Reviews, editorials, and book chapters

• Designing an open-source microscope Aharoni D The Transmitter, 2024 · doi:10.53053/HWXJ2956
• Special Section Guest Editorial: Open-source neurophotonic tools for neuroscience Kodandaramaiah SB, Aharoni D, Gibson EA Neurophotonics, 11(3), September 2024 · doi:10.1117/1.NPh.11.3.034301
• Miniaturized microscopy as a tool to track neuronal population dynamics in epilepsy models Aharoni D, Golshani P Book chapter in Engel J (ed.), Epilepsy: A Comprehensive Textbook, 2023
• Circuit investigations with open-source miniaturized microscopes: past, present and future Aharoni D, Hoogland TM Frontiers in Cellular Neuroscience, March 2019 · doi:10.3389/fncel.2019.00141
• All the light that we can see: a new era in miniaturized microscopy Aharoni D, Khakh BS, Silva AJ, Golshani P Nature Methods, December 2018 · doi:10.1038/s41592-018-0266-x

Conference proceedings

• Wireless power transfer for neural recording devices in freely behaving animals: current solutions and future directions Aharoni D, Brosch M, Sasatani T Proc. SPIE 13889, Optical Power Delivery II, 9–13, January 2026
• All-optical network-scale neural imaging and optogenetic control at neuronal resolution Chorsi H, Soldado-Magraner S, Jin Y, Golshani P, Buonomano DV, Aharoni D Optics and the Brain, BS1A.3, 2026
• STIMscope: an open-source real-time imaging and patterned illumination framework Chorsi H, Soldado-Magraner S, Lu L, Dan Y, Buonomano DV, Aharoni D European Conference on Biomedical Optics (ECBO), W1C.2, 2025
• Introducing the STIMscope: an open-source platform for large field-of-view spatiotemporal imaging and patterned illumination Chorsi HT, Soldado-Magraner S, Sangiuliano Jimka FN, Buonomano DV, Markovic D, Aharoni D Proc. SPIE Optics + Photonics, 2024
• High-throughput single-molecule fluorescence spectroscopy using parallel detection 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, Chioni M, Tisa S, Zappa F, Cova S, Weiss S Proc. SPIE 7608, 2010 · doi:10.1117/12.846784

Patents

• System and method for configurable miniature microscopy Aharoni D WO/2018/213255, 2018