@article {68968, title = {Ultra-high density electrodes improve detection, yield, and cell type specificity of brain recordings.}, journal = {bioRxiv}, year = {2023}, month = {2023 Aug 25}, abstract = {

To study the neural basis of behavior, we require methods to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology is a principal method for achieving this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To overcome these limitations, we developed a silicon probe with significantly smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device measures neuronal activity at ultra-high densities (\>1300 sites per mm, 10 times higher than previous probes), with 6 {\textmu}m center-to-center spacing and low noise. This device effectively comprises an implantable voltage-sensing camera that captures a planar image of a neuron{\textquoteright}s electrical field. We introduce a new spike sorting algorithm optimized for these probes and use it to find that the yield of visually-responsive neurons in recordings from mouse visual cortex improves \~{}3-fold. Recordings across multiple brain regions and four species revealed a subset of unexpectedly small extracellular action potentials not previously reported. Further experiments determined that, in visual cortex, these do not correspond to major subclasses of interneurons and instead likely reflect recordings from axons. Finally, using ground-truth identification of cortical inhibitory cell types with optotagging, we found that cell type was discriminable with approximately 75\% success among three types, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, sampling bias, and cell type classification.

}, doi = {10.1101/2023.08.23.554527}, author = {Ye, Zhiwen and Shelton, Andrew M and Shaker, Jordan R and Boussard, Julien and Colonell, Jennifer and Manavi, Sahar and Chen, Susu and Windolf, Charlie and Hurwitz, Cole and Namima, Tomoyuki and Pedraja, Federico and Weiss, Shahaf and Raducanu, Bogdan and Ness, Torbj{\o}rn V and Einevoll, Gaute T and Laurent, Gilles and Sawtell, Nathaniel B and Bair, Wyeth and Pasupathy, Anitha and Mora Lopez, Carolina and Dutta, Barun and Paninski, Liam and Siegle, Joshua H and Koch, Christof and Olsen, Shawn R and Harris, Timothy D and Steinmetz, Nicholas A} } @article {47134, title = {Neural encoding of odors during active sampling and in turbulent plumes.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Oct 21}, pages = {403-18}, abstract = {

Sensory inputs are often fluctuating and intermittent, yet animals reliably utilize them to direct behavior. Here we ask how natural stimulus fluctuations influence the dynamic neural encoding of odors. Using the locust olfactory system, we isolated two main causes of odor intermittency: chaotic odor plumes and active sampling behaviors. Despite their irregularity, chaotic odor plumes still drove dynamic neural response features including the synchronization, temporal patterning, and short-term plasticity of spiking in projection neurons, enabling classifier-based stimulus identification and activating downstream decoders (Kenyon cells). Locusts can also impose odor intermittency through active sampling movements with their unrestrained antennae. Odors triggered immediate, spatially targeted antennal scanning that, paradoxically, weakened individual neural responses. However, these frequent but weaker responses were highly informative about stimulus location. Thus, not only are odor-elicited dynamic neural responses compatible with natural stimulus fluctuations and important for stimulus identification, but locusts actively increase intermittency, possibly to improve stimulus localization.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.09.007}, author = {Huston, Stephen J and Stopfer, Mark and Cassenaer, Stijn and Aldworth, Zane N and Laurent, Gilles} } @inbook {3326, title = {Circuit dynamics and neural coding in the locust olfactory system.}, booktitle = {The New Encyclopedia of Neuroscience}, year = {2009}, publisher = {Elsevier Science}, organization = {Elsevier Science}, address = {Oxford}, author = {Jayaraman, Vivek and Laurent, Gilles} } @article {47223, title = {Olfactory representations by Drosophila mushroom body neurons.}, journal = {Journal of Neurophysiology}, volume = {99}, year = {2008}, month = {2008 Feb}, pages = {734-46}, abstract = {

Learning and memory has been studied extensively in Drosophila using behavioral, molecular, and genetic approaches. These studies have identified the mushroom body as essential for the formation and retrieval of olfactory memories. We investigated odor responses of the principal neurons of the mushroom body, the Kenyon cells (KCs), in Drosophila using whole cell recordings in vivo. KC responses to odors were highly selective and, thus sparse, compared with those of their direct inputs, the antennal lobe projection neurons (PNs). We examined the mechanisms that might underlie this transformation and identified at least three contributing factors: excitatory synaptic potentials (from PNs) decay rapidly, curtailing temporal integration, PN convergence onto individual KCs is low ( approximately 10 PNs per KC on average), and KC firing thresholds are high. Sparse activity is thought to be useful in structures involved in memory in part because sparseness tends to reduce representation overlaps. By comparing activity patterns evoked by the same odors across olfactory receptor neurons and across KCs, we show that representations of different odors do indeed become less correlated as they progress through the olfactory system.

}, keywords = {Anesthetics, Local, Animals, Brain Mapping, Drosophila, Electric Stimulation, Excitatory Postsynaptic Potentials, Membrane Potentials, Mushroom Bodies, Nerve Net, Neurons, Afferent, Odors, Olfactory Pathways, Patch-Clamp Techniques, Spectrum Analysis, Tetrodotoxin}, issn = {0022-3077}, doi = {10.1152/jn.01283.2007}, author = {Turner, Glenn C and Bazhenov, Maxim and Laurent, Gilles} } @article {1647, title = {Evaluating a genetically encoded optical sensor of neural activity using electrophysiology in intact adult fruit flies.}, journal = {Frontiers in Neural Circuits}, volume = {1}, year = {2007}, month = {2007 Nov 2}, pages = {3}, abstract = {

Genetically encoded optical indicators hold the promise of enabling non-invasive monitoring of activity in identified neurons in behaving organisms. However, the interpretation of images of brain activity produced using such sensors is not straightforward. Several recent studies of sensory coding used G-CaMP 1.3-a calcium sensor-as an indicator of neural activity; some of these studies characterized the imaged neurons as having narrow tuning curves, a conclusion not always supported by parallel electrophysiological studies. To better understand the possible cause of these conflicting results, we performed simultaneous in vivo 2-photon imaging and electrophysiological recording of G-CaMP 1.3 expressing neurons in the antennal lobe (AL) of intact fruitflies. We find that G-CaMP has a relatively high threshold, that its signal often fails to capture spiking response kinetics, and that it can miss even high instantaneous rates of activity if those are not sustained. While G-CaMP can be misleading, it is clearly useful for the identification of promising neural targets: when electrical activity is well above the sensor{\textquoteright}s detection threshold, its signal is fairly well correlated with mean firing rate and G-CaMP does not appear to alter significantly the responses of neurons that express it. The methods we present should enable any genetically encoded sensor, activator, or silencer to be evaluated in an intact neural circuit in vivo in Drosophila.

}, issn = {1662-5110}, doi = {10.3389/neuro.04.003.2007}, author = {Jayaraman, Vivek and Laurent, Gilles} } @article {1648, title = {Encoding and decoding of overlapping odor sequences.}, journal = {Neuron}, volume = {51}, year = {2005}, month = {2006 Aug 17}, pages = {467-82}, abstract = {

Odors evoke complex responses in locust antennal lobe projection neurons (PNs)-the mitral cell analogs. These patterns evolve over hundreds of milliseconds and contain information about odor identity and concentration. In nature, animals often encounter many odorants in short temporal succession. We explored the effects of such conditions by presenting two different odors with variable intervening delays. PN ensemble representations tracked stimulus changes and, in some delay conditions, reached states that corresponded neither to the representation of either odor alone nor to the static mixture of the two. We then recorded from Kenyon cells (KCs), the PNs{\textquoteright} targets. Their responses were consistent with the PN population{\textquoteright}s behavior: in some conditions, KCs were recruited that did not fire during single-odor or mixture stimuli. Thus, PN population dynamics are history dependent, and responses of individual KCs are consistent with piecewise temporal decoding of PN output over large sections of the PN population.

}, keywords = {Action Potentials, Afferent, Afferent Pathways, Animals, Chemical, Discrimination (Psychology), Locusta migratoria, Male, Neural Inhibition, Neurons, Odors, Reaction Time, Sense Organs, Stimulation, Time Factors}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.07.018}, author = {Broome, Bede M and Jayaraman, Vivek and Laurent, Gilles} } @article {47224, title = {Transformation of olfactory representations in the Drosophila antennal lobe.}, journal = {Science (New York, N.Y.)}, volume = {303}, year = {2004}, month = {2004 Jan 16}, pages = {366-70}, abstract = {

Molecular genetics has revealed a precise stereotypy in the projection of primary olfactory sensory neurons onto secondary neurons. A major challenge is to understand how this mapping translates into odor responses in these second-order neurons. We investigated this question in Drosophila using whole-cell recordings in vivo. We observe that monomolecular odors generally elicit responses in large ensembles of antennal lobe neurons. Comparison of odor-evoked activity from afferents and postsynaptic neurons in the same glomerulus revealed that second-order neurons display broader tuning and more complex responses than their primary afferents. This indicates a major transformation of odor representations, implicating lateral interactions within the antennal lobe.

}, keywords = {Action Potentials, Animals, Drosophila, Excitatory Postsynaptic Potentials, GABA Antagonists, GABA-A Receptor Antagonists, Nervous System Physiological Phenomena, Neural Inhibition, Neurons, Afferent, Odors, Olfactory Pathways, Olfactory Receptor Neurons, Patch-Clamp Techniques, Picrotoxin, Receptors, GABA-A, Sense Organs, Smell, Synapses}, issn = {1095-9203}, doi = {10.1126/science.1090782}, author = {Wilson, Rachel I and Turner, Glenn C and Laurent, Gilles} } @article {1649, title = {Intensity versus identity coding in an olfactory system.}, journal = {Neuron}, volume = {39}, year = {2003}, month = {2003 Sep 11}, pages = {991-1004}, abstract = {

We examined the encoding and decoding of odor identity and intensity by neurons in the antennal lobe and the mushroom body, first and second relays, respectively, of the locust olfactory system. Increased odor concentration led to changes in the firing patterns of individual antennal lobe projection neurons (PNs), similar to those caused by changes in odor identity, thus potentially confounding representations for identity and concentration. However, when these time-varying responses were examined across many PNs, concentration-specific patterns clustered by identity, resolving the apparent confound. This is because PN ensemble representations changed relatively continuously over a range of concentrations of each odorant. The PNs{\textquoteright} targets in the mushroom body-Kenyon cells (KCs)-had sparse identity-specific responses with diverse degrees of concentration invariance. The tuning of KCs to identity and concentration and the patterning of their responses are consistent with piecewise decoding of their PN inputs over oscillation-cycle length epochs.

}, keywords = {Action Potentials, Animals, Female, Grasshoppers, Male, Mushroom Bodies, Neurons, Odors, Reaction Time, Smell}, issn = {0896-6273}, author = {Stopfer, Mark and Jayaraman, Vivek and Laurent, Gilles} } @article {47225, title = {Oscillations and sparsening of odor representations in the mushroom body.}, journal = {Science (New York, N.Y.)}, volume = {297}, year = {2002}, month = {2002 Jul 19}, pages = {359-65}, abstract = {

In the insect olfactory system, oscillatory synchronization is functionally relevant and reflects the coherent activation of dynamic neural assemblies. We examined the role of such oscillatory synchronization in information transfer between networks in this system. The antennal lobe is the obligatory relay for olfactory afferent signals and generates oscillatory output. The mushroom body is responsible for formation and retrieval of olfactory and other memories. The format of odor representations differs significantly across these structures. Whereas representations are dense, dynamic, and seemingly redundant in the antennal lobe, they are sparse and carried by more selective neurons in the mushroom body. This transformation relies on a combination of oscillatory dynamics and intrinsic and circuit properties that act together to selectively filter and synthesize the output from the antennal lobe. These results provide direct support for the functional relevance of correlation codes and shed some light on the role of oscillatory synchronization in sensory networks.

}, keywords = {Action Potentials, Animals, Electric Stimulation, Electrodes, Evoked Potentials, Excitatory Postsynaptic Potentials, Female, gamma-Aminobutyric Acid, Grasshoppers, Interneurons, Male, Mushroom Bodies, Nerve Net, Neural Inhibition, Neurons, Odors, Patch-Clamp Techniques, Picrotoxin, Smell, Synaptic Transmission, Time Factors}, issn = {1095-9203}, doi = {10.1126/science.1070502}, author = {Perez-Orive, Javier and Mazor, Ofer and Turner, Glenn C and Cassenaer, Stijn and Wilson, Rachel I and Laurent, Gilles} }