@article {65364, title = {Recurrent interactions in local cortical circuits.}, journal = {Nature}, volume = {579}, year = {2020}, month = {2020 Mar 04}, pages = {256-59}, abstract = {

Most cortical synapses are local and excitatory. Local recurrent circuits could implement amplification, allowing pattern completion and other computations. Cortical circuits contain subnetworks that consist of neurons with similar receptive fields and increased connectivity relative to the network average. Cortical neurons that encode different types of information are spatially intermingled and distributed over large brain volumes, and this complexity has hindered attempts to probe the function of these subnetworks by perturbing them individually. Here we use computational modelling, optical recordings and manipulations to probe the function of recurrent coupling in layer 2/3 of the mouse vibrissal somatosensory cortex during active tactile discrimination. A neural circuit model of layer 2/3 revealed that recurrent excitation enhances sensory signals by amplification, but only for subnetworks with increased connectivity. Model networks with high amplification were sensitive to damage: loss of a few members of the subnetwork degraded stimulus encoding. We tested this prediction by mapping neuronal selectivity and photoablating neurons with specific selectivity. Ablation of a small proportion of layer 2/3 neurons (10-20, less than 5\% of the total) representing touch markedly reduced responses in the spared touch representation, but not in other representations. Ablations most strongly affected neurons with stimulus responses that were similar to those of the ablated population, which is also consistent with network models. Recurrence among cortical neurons with similar selectivity therefore drives input-specific amplification during behaviour.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2062-x}, author = {Peron, Simon and Pancholi, Ravi and Voelcker, Bettina and Wittenbach, Jason D and {\'O}lafsd{\'o}ttir, H Freyja and Freeman, Jeremy and Svoboda, Karel} } @article {46590, title = {Comprehensive imaging of cortical networks.}, journal = {Current Opinion in Neurobiology}, volume = {32}, year = {2015}, month = {2015 Apr 10}, pages = {115-123}, abstract = {

Neural computations are implemented by activity in spatially distributed neural circuits. Cellular imaging fills a unique niche in linking activity of specific types of neurons to behavior, over spatial scales spanning single neurons to entire brain regions, and temporal scales from milliseconds to months. Imaging may soon make it possible to track activity of all neurons in a brain region, such as a cortical column. We review recent methodological advances that facilitate optical imaging of neuronal populations in vivo, with an emphasis on calcium imaging using protein indicators in mice. We point out areas that are particularly ripe for future developments.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.03.016}, author = {Peron, Simon and Chen, Tsai-Wen and Svoboda, Karel} } @article {47158, title = {Neurodata without borders: creating a common data format for neurophysiology}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Nov 18}, pages = {629-34}, abstract = {

The Neurodata Without Borders (NWB) initiative promotes data standardization in neuroscience to increase research reproducibility and opportunities. In the first NWB pilot project, neurophysiologists and software developers produced a common data format for recordings and metadata of cellular electrophysiology and optical imaging experiments. The format specification, application programming interfaces, and sample datasets have been released.

}, doi = {10.1016/j.neuron.2015.10.025}, author = {Teeters, Jeffrey L and Godfrey, Keith and Young, Rob and Dang, Chinh and Friedsam, Claudia and Wark, Barry and Asari, Hiroki and Peron, Simon and Li, Nuo and Peyrache, Adrien} } @article {6897, title = {Procedures for behavioral experiments in head-fixed mice.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e88678}, abstract = {

The mouse is an increasingly prominent model for the analysis of mammalian neuronal circuits. Neural circuits ultimately have to be probed during behaviors that engage the circuits. Linking circuit dynamics to behavior requires precise control of sensory stimuli and measurement of body movements. Head-fixation has been used for behavioral research, particularly in non-human primates, to facilitate precise stimulus control, behavioral monitoring and neural recording. However, choice-based, perceptual decision tasks by head-fixed mice have only recently been introduced. Training mice relies on motivating mice using water restriction. Here we describe procedures for head-fixation, water restriction and behavioral training for head-fixed mice, with a focus on active, whisker-based tactile behaviors. In these experiments mice had restricted access to water (typically 1 ml/day). After ten days of water restriction, body weight stabilized at approximately 80\% of initial weight. At that point mice were trained to discriminate sensory stimuli using operant conditioning. Head-fixed mice reported stimuli by licking in go/no-go tasks and also using a forced choice paradigm using a dual lickport. In some cases mice learned to discriminate sensory stimuli in a few trials within the first behavioral session. Delay epochs lasting a second or more were used to separate sensation (e.g. tactile exploration) and action (i.e. licking). Mice performed a variety of perceptual decision tasks with high performance for hundreds of trials per behavioral session. Up to four months of continuous water restriction showed no adverse health effects. Behavioral performance correlated with the degree of water restriction, supporting the importance of controlling access to water. These behavioral paradigms can be combined with cellular resolution imaging, random access photostimulation, and whole cell recordings.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0088678}, author = {Guo, Zengcai V and Hires, S Andrew and Li, Nuo and O{\textquoteright}Connor, Daniel H and Komiyama, Takaki and Ophir, Eran and Huber, Daniel and Bonardi, Claudia and Morandell, Karin and Gutnisky, Diego and Peron, Simon and Xu, Ning-long and Cox, James and Svoboda, Karel} } @article {5200, title = {Automated tracking of whiskers in videos of head fixed rodents.}, journal = {PLoS Computational Biology}, volume = {8}, year = {2012}, month = {2012 Jul}, pages = {e1002591}, abstract = {

We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (\>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998\% and identifies individual whiskers with 99.997\% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px{\texttimes}352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002591}, author = {Clack, Nathan G and O{\textquoteright}Connor, Daniel H and Huber, Daniel and Petreanu, Leopoldo and Hires, Andrew and Peron, Simon and Svoboda, Karel and Myers, Eugene W} } @article {4307, title = {From cudgel to scalpel: toward precise neural control with optogenetics.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Jan}, pages = {30-4}, abstract = {

Optogenetics is routinely used to activate and inactivate genetically defined neuronal populations in vivo. A second optogenetic revolution will occur when spatially distributed and sparse neural assemblies can be precisely manipulated in behaving animals.

}, keywords = {Animals, Gene Expression Regulation, Genetic Techniques, Light, Neurons, Organ Specificity, Photic Stimulation}, issn = {1548-7105}, doi = {10.1038/nmeth.f.325}, author = {Peron, Simon and Svoboda, Karel} }