Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals DOI Creative Commons

Olav Stetter,

Demian Battaglia, Jordi Soriano

et al.

PLoS Computational Biology, Journal Year: 2012, Volume and Issue: 8(8), P. e1002653 - e1002653

Published: Aug. 23, 2012

A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically unfeasible even in dissociated neuronal cultures. We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct approximations structural connectivities from activity monitored calcium fluorescence imaging. Based information theory, our method requires no prior assumptions the statistics firing and connections. The performance algorithm is benchmarked surrogate time-series generated by simulated dynamics a with known ground-truth topology. find that effective topology revealed depends qualitatively time-dependent dynamic state (e.g., bursting or non-bursting). thus demonstrate how conditioning respect mean improves method. [...] Compared other reconstruction strategies such as cross-correlation Granger Causality methods, remarkably more accurate. In particular, it provides good clustering coefficient, allowing discriminate between weakly strongly clustered topologies, whereas hand cross-correlations would invariantly detect artificially high levels clustering. Finally, we present applicability real recordings vitro cortical these networks are characterized elevated level compared random graph (although not extreme) markedly non-local connectivity.

Language: Английский

A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging DOI Creative Commons
Nicholas Sofroniew, Daniel Flickinger, Jonathan King

et al.

eLife, Journal Year: 2016, Volume and Issue: 5

Published: June 14, 2016

Imaging is used to map activity across populations of neurons. Microscopes with cellular resolution have small (<1 millimeter) fields view and cannot simultaneously image distributed multiple brain areas. Typical large field microscopes do not resolve single cells, especially in the axial dimension. We developed a 2-photon random access mesoscope (2p-RAM) that allows high-resolution imaging anywhere within volume spanning areas (∅ 5 mm x 1 cylinder). 2p-RAM near diffraction limited (lateral, 0.66 μm, 4.09 μm at center; excitation wavelength = 970 nm; numerical aperture 0.6) over range wavelengths. A fast three-dimensional scanning system efficient sampling neural arbitrary regions interest entire volume. illustrate use by multiple, non-contiguous transgenic mice expressing protein calcium sensors.

Language: Английский

Citations

645

Genetically encoded indicators of neuronal activity DOI
Michael Z. Lin, Mark J. Schnitzer

Nature Neuroscience, Journal Year: 2016, Volume and Issue: 19(9), P. 1142 - 1153

Published: Aug. 26, 2016

Language: Английский

Citations

626

The Brain Activity Map Project and the Challenge of Functional Connectomics DOI Creative Commons
A. Paul Alivisatos,

Miyoung Chun,

George M. Church

et al.

Neuron, Journal Year: 2012, Volume and Issue: 74(6), P. 970 - 974

Published: June 1, 2012

Language: Английский

Citations

573

Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo DOI
Adam M. Packer, Lloyd Russell, Henry Dalgleish

et al.

Nature Methods, Journal Year: 2014, Volume and Issue: 12(2), P. 140 - 146

Published: Dec. 22, 2014

Language: Английский

Citations

556

Fast online deconvolution of calcium imaging data DOI Creative Commons
Johannes Friedrich, Pengcheng Zhou, Liam Paninski

et al.

PLoS Computational Biology, Journal Year: 2017, Volume and Issue: 13(3), P. e1005423 - e1005423

Published: March 14, 2017

Fluorescent calcium indicators are a popular means for observing the spiking activity of large neuronal populations, but extracting each neuron from raw fluorescence imaging data is nontrivial problem. We present fast online active set method to solve this sparse non-negative deconvolution Importantly, algorithm progresses through time series sequentially beginning end, thus enabling real-time estimation neural during session. Our generalization pool adjacent violators (PAVA) isotonic regression and inherits its linear-time computational complexity. gain remarkable increases in processing speed: more than one order magnitude compared currently employed state art convex solvers relying on interior point methods. Unlike these approaches, our can exploit warm starts; therefore optimizing model hyperparameters only requires handful passes data. A minor modification further improve quality inference by imposing constraint minimum spike size. The enables simultaneous $O(10^5)$ traces whole-brain larval zebrafish laptop.

Language: Английский

Citations

539

Optical magnetic detection of single-neuron action potentials using quantum defects in diamond DOI Open Access
John F. Barry, Matthew Turner, Jennifer M. Schloss

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2016, Volume and Issue: 113(49), P. 14133 - 14138

Published: Nov. 22, 2016

Significance We demonstrate noninvasive detection of action potentials with single-neuron sensitivity, including in whole organisms. Our sensor is composed quantum defects within a diamond chip, which detect time-varying magnetic fields generated by potentials. The biocompatible and can be brought into close proximity to the organism without adverse effect, allowing for long-term observation superior resolution neuron fields. Optical also provides information about potential propagation that not easily available existing methods. technique requires no labeling or genetic modification, allows submillisecond time resolution, does bleach, senses through opaque tissue. With further development, we expect micrometer-scale imaging variety neuronal phenomena.

Language: Английский

Citations

532

In Vivo Evidence for a Lactate Gradient from Astrocytes to Neurons DOI Creative Commons
Philipp Mächler, Matthias T. Wyss,

Maha Elsayed

et al.

Cell Metabolism, Journal Year: 2015, Volume and Issue: 23(1), P. 94 - 102

Published: Nov. 19, 2015

Language: Английский

Citations

512

Fast and sensitive GCaMP calcium indicators for imaging neural populations DOI Creative Commons
Yan Zhang,

Márton Rózsa,

Yajie Liang

et al.

Nature, Journal Year: 2023, Volume and Issue: 615(7954), P. 884 - 891

Published: March 15, 2023

Abstract Calcium imaging with protein-based indicators 1,2 is widely used to follow neural activity in intact nervous systems, but current protein sensors report at timescales much slower than electrical signalling and are limited by trade-offs between sensitivity kinetics. Here we large-scale screening structure-guided mutagenesis develop optimize several fast sensitive GCaMP-type 3–8 . The resulting ‘jGCaMP8’ sensors, based on the calcium-binding calmodulin a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (half-rise times 2 ms) highest for reported calcium sensor. jGCaMP8 will allow tracking large populations neurons relevant computation.

Language: Английский

Citations

466

Genetic Dissection of Neural Circuits: A Decade of Progress DOI Creative Commons
Liqun Luo, Edward M. Callaway, Karel Svoboda

et al.

Neuron, Journal Year: 2018, Volume and Issue: 98(2), P. 256 - 281

Published: April 1, 2018

Tremendous progress has been made since Neuron published our Primer on genetic dissection of neural circuits 10 years ago. Since then, cell-type-specific anatomical, neurophysiological, and perturbation studies have carried out in a multitude invertebrate vertebrate organisms, linking neurons to behavioral functions. New methods allow systematic classification cell types provide access diverse neuronal for connectivity coding during behavior. Here we evaluate key advances over the past decade discuss future directions.

Language: Английский

Citations

453

Astrocyte Ca2+ signalling: an unexpected complexity DOI
Andrea Volterra, Nicolas Liaudet, Iaroslav Savtchouk

et al.

Nature reviews. Neuroscience, Journal Year: 2014, Volume and Issue: 15(5), P. 327 - 335

Published: April 17, 2014

Language: Английский

Citations

430