Publications

2026
bioRxiv Zapit: open source random-access photostimulation for neuroscience M Lohse*, OM Gauld*, MT Quigley*, A Masood*, C Bao, J Li, NJ Miska, G Nabbefeld, Q Pajot-Moric, S Townsend, P Vincent, AY Yang, N Zervogiannis, A Akrami, CA Duan, JC Erlich, SB Hofer, TD Mrsic-Flogel, P Coen‡, RAA Campbell‡ * equal contribution · ‡ equal senior authors Opsins provide millisecond-precision control over genetically defined neural populations, but targeted light delivery remains technically challenging. We present Zapit, a complete open-source platform for spatiotemporally precise random-access laser-scanning optogenetic experiments in head-fixed mice. The system enables flexible targeting of distributed cortical areas without invasive fibre implantation. We describe the hardware and software, quantify its performance, validate physiological effects on cortical activity, and demonstrate proof-of-principle cortical photoinhibition experiments in behaving mice. [Summary courtesy of ClaudioVisual]
2025
eLife The SAFE Labs Handbook as a tool for improving lab culture ED Donà, JM Gahan, P Lau, J Jeschke, T Ott, K Reinhard, C Sinigaglia, JL Treur, T Vogl, S Bugeon*, L Mariotti*, LF Rossi*, P Coen* * equal contribution The SAFE Labs Handbook is a collection of 30 commitments that can be implemented by individual group leaders to improve research culture in the life sciences. Collaboratively developed by 13 group leaders across eight European countries, it covers areas including onboarding, mentoring, feedback, and wellbeing. A survey of over 200 researchers found all 30 commitments were rated as significantly important, yet implementation rates were below 25%, though more than 95% of group leaders said they would consider adopting them. [Summary courtesy of ClaudioVisual]
2025
Nature Methods Tracking neurons across days with high-density probes EH van Beest*, C Bimbard*, JMJ Fabre, SW Dodgson, F Takács, P Coen, A Lebedeva, KD Harris, M Carandini * equal contribution UnitMatch is a pipeline for tracking neurons across days in chronic Neuropixels recordings, operating after spike sorting based only on each unit's average spike waveform. It does not require simultaneously recorded data or additional hardware. Tested in mouse brain, UnitMatch tracked neurons across weeks, revealing stable inter-spike interval distributions and visual selectivity in visual cortex, but changing neuronal responses in the striatum during task learning, demonstrating its value for studying long-term neural dynamics. [Summary courtesy of ClaudioVisual]
2025
eLife An adaptable, reusable, and light implant for chronic Neuropixels probes C Bimbard, F Takács, JA Catarino, JMJ Fabre, S Gupta, SC Lenzi, M Melin, N O'Neill, I Orsolic, M Robacha, JS Street, J Teixeira, S Townsend, EH van Beest, AM Zhang, AK Churchland, CA Duan, KD Harris, DM Kullmann, G Lignani, ZF Mainen, TW Margrie, NL Rochefort, AM Wikenheiser, M Carandini, P Coen The Apollo Implant is an open-source device for chronic Neuropixels 1.0 and 2.0 probe implantation, comprising a recoverable "payload" module attached to the probe and a "docking" module cemented to the skull. 3D-printed and lightweight, it enables stable neuron recordings over weeks with full probe recovery and reimplantation without reduction in recording quality. Successfully tested across eight laboratories in both head-fixed and freely moving mice and rats, it provides an affordable and flexible solution for chronic electrophysiology. [Summary courtesy of ClaudioVisual]
2025
bioRxiv Functional dissociation of layers 2/3 and 5 in the primary visual cortex TPH Sit, C Bimbard, A Lebedeva, M Carandini, P Coen, KD Harris Using large-scale two-photon calcium imaging and Neuropixels recordings, we show that mouse primary visual cortex integrates visual and non-visual information differently across layers. Layer 2/3 activity is more strongly modulated by visual stimuli, whereas layer 5 is more strongly modulated by the animal's movement. Movement has opposite effects on population synchrony: it desynchronizes layer 2/3 spontaneous oscillations while synchronizing layer 5. These results suggest a division of labour where superficial layers generate robust sensory representations while deep layers integrate sensory signals with behavioural context. [Summary courtesy of ClaudioVisual]
2023
Neuron Mouse frontal cortex mediates additive multisensory decisions P Coen*, TPH Sit*, MJ Wells, M Carandini‡, KD Harris‡ * equal contribution · ‡ co-senior authors We trained mice to make decisions based on combined auditory and visual stimuli and found that frontal cortex combines evidence from both modalities additively, mirroring the animals' behaviour. This multisensory combination evolves with learning. Inactivating frontal cortex impaired responses to either modality, and recordings from over 14,000 neurons revealed that anterior frontal area MOs additively encodes visual and auditory signals specifically after task learning, establishing frontal cortex as the site where multisensory evidence is combined for decision-making. [Summary courtesy of ClaudioVisual]
2018
Current Biology Discovery of a new song mode in Drosophila reveals hidden structure in the sensory and neural drivers of behavior J Clemens*, P Coen*, FA Roemschied*, TD Pereira, D Mazumder, DE Aldarondo, DA Pacheco, M Murthy * equal contribution Using unsupervised classification on large datasets of Drosophila melanogaster courtship song, we establish that the song consists of at least three modes, not the two (sine and pulse) recognised for 50 years. The newly identified modes — Pslow (low frequency, symmetrical pulses) and Pfast (faster, asymmetrical pulses) — are produced in different behavioural contexts and driven by distinct sensory cues, revealing previously hidden structure in the sensory and neural drivers of acoustic communication behaviour. [Summary courtesy of ClaudioVisual]
2017
PNAS Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms DL Stern, J Clemens, P Coen, AJ Calhoun, JB Hogenesch, BJ Arthur, M Murthy For decades, it was believed that Drosophila courtship songs contain periodic rhythms controlled by the period gene, and that rhythm differences between species contribute to reproductive isolation. We experimentally and statistically reevaluate this claim using manually annotated data, automatically segmented data, and a new large-scale dataset. Across all analyses, we find no evidence for the existence of song rhythms or periodicity differences between genotypes, overturning a long-standing assumption in the field. [Summary courtesy of ClaudioVisual]
2017
eNeuro Aberrant cortical activity in multiple GCaMP6-expressing transgenic mouse lines NA Steinmetz, C Buetfering, J Lecoq, CR Lee, AJ Peters, EAK Jacobs, P Coen, DR Ollerenshaw, MT Valley, SEJ De Vries, M Garrett, J Zhuang, PA Groblewski, S Manavi, J Miles, C White, E Lee, F Griffin, JD Larkin, K Roll, S Cross, TV Nguyen, R Larsen, J Pendergraft, T Daigle, B Tasic, CL Thompson, J Waters, S Olsen, DJ Margolis, H Zeng, M Bhatt, M Carandini, KD Harris Certain transgenic mouse lines expressing the calcium indicator GCaMP6, particularly those carrying Emx1-Cre and Ai93 transgenes, display aberrant epileptiform electrical activity resembling interictal spikes at frequencies exceeding 0.1 Hz with amplitudes surpassing 1.0 mV. While most neuronal responses and behavioural patterns appear normal despite these events, some subjects display overt generalised seizures. These findings highlight the importance of carefully selecting appropriate transgenic models and screening for aberrant activity in calcium imaging studies. [Summary courtesy of ClaudioVisual]
2016
Current Opinion in Neurobiology Singing on the fly: sensorimotor integration and acoustic communication in Drosophila P Coen, M Murthy This review covers recent advances in understanding acoustic communication in Drosophila melanogaster, where new methods for high-throughput behavioural analysis and powerful genetic tools have enabled detailed studies of how flies produce and process time-varying courtship sounds. We discuss how sensory feedback from the female plays a critical role in dynamically shaping male song production, and how the neural circuits underlying song generation and auditory processing are beginning to be identified, laying the foundation for understanding how sensory information modulates behaviour in real time. [Summary courtesy of ClaudioVisual]
2016
Neuron Sensorimotor transformations underlying variability in song intensity during Drosophila courtship P Coen, M Xie, J Clemens, M Murthy Drosophila males dynamically modulate courtship song amplitude as a function of their distance to the female. We investigate each stage of the sensorimotor transformation underlying this behaviour, from visual detection of the female through to modulation of neural and muscle activity patterns. Our results reveal a dual output of the song central pattern generator that independently controls pulse rate and amplitude via direct and indirect flight muscles, demonstrating that song intensity is regulated independently from spectral and temporal features. [Summary courtesy of ClaudioVisual]
2015
Neuron Connecting neural codes with behavior in the auditory system of Drosophila J Clemens*, CC Girardin*, P Coen, X Guan, BJ Dickson, M Murthy * equal contribution We use computational modelling to link natural Drosophila courtship song, neuronal codes, and female behavioural responses. Intracellular recordings reveal how auditory neurons encode song features, and we show that females are sensitive to song structure over timescales of tens of seconds. Using a simple decoder applied to neural responses, we can predict female behavioural responses to natural song with high accuracy, providing a quantitative framework for connecting neural representations to behaviour in this system. [Summary courtesy of ClaudioVisual]
2014
Nature Dynamic sensory cues shape song structure in Drosophila P Coen, J Clemens, A Weinstein, DA Pacheco, Y Deng, M Murthy It was previously believed that Drosophila courtship songs had relatively fixed structures, with variability arising from neural noise. Using a quantitative behavioural assay and computational modelling, we show instead that males use fast changes in visual and self-motion sensory information to actively pattern individual song sequences in real time. This sensorimotor relationship is evolutionarily conserved across Drosophila species, and we identify the neural pathways involved in translating sensory cues into song patterning decisions. [Summary courtesy of ClaudioVisual]
2013
PLoS One Efficient multiple object tracking using mutually repulsive active membranes Y Deng, P Coen, M Sun, JW Shaevitz We adopt an open active contour model with repulsive interactions to track trajectories of moving objects at high density, applied to Drosophila walking behaviour and bacterial gliding. The algorithm achieves error rates better than 0.1% per fly per second at densities of up to 20 animals in a small arena. Analysis of the resulting trajectories demonstrates that individual male flies have distinct walking signatures and that social interactions in mixed-gender arenas are gender-specific. [Summary courtesy of ClaudioVisual]
2013
BMC Biology Multi-channel acoustic recording and automated analysis of Drosophila courtship songs BJ Arthur, T Sunayama-Morita, P Coen, M Murthy‡, DL Stern‡ ‡ co-senior authors We present a sensitive 32-channel microphone array system to simultaneously capture acoustic signals from 32 separate pairs of courting Drosophila, along with software for automated song segmentation and feature extraction. Applied to over 18 hours of courtship song from five wild-type strains, the analysis revealed previously undetected modulation of song features including amplitude and inter-pulse interval, as well as extensive natural genetic variation for most song components across strains. [Summary courtesy of ClaudioVisual]
2012
Journal of Neuroscience Neural representations of courtship song in the Drosophila brain S Tootoonian, P Coen, R Kawai, M Murthy We used intracellular recordings from neurons in the antennal mechanosensory and motor centre (AMMC) to characterise how courtship song is represented in the Drosophila brain. Steady-state responses to tones and broadband noise undergo significant transformation between receptor and central neurons, but transient responses to individual song pulses are largely preserved. AMMC neurons apply low-pass filtering to receptor signals, selectively maintaining the temporal structure of natural stimuli relevant for downstream behavioural processing. [Summary courtesy of ClaudioVisual]
2012
Nature Choice-specific sequences in parietal cortex during a virtual-navigation decision task C Harvey, P Coen, DW Tank We used optical imaging to monitor neuronal populations in mouse posterior parietal cortex during a virtual-navigation decision task. Individual neurons had brief, transient activations at different moments during the trial, forming sequences that spanned the entire task period. Crucially, distinct neuronal sequences were triggered on trials with opposite behavioural choices, defining divergent, choice-specific trajectories through a high-dimensional space of population activity that could be used to predict the animal's upcoming decision. [Summary courtesy of ClaudioVisual]