scholarly journals Scalable and accurate automated method for neuronal ensemble detection in spiking neural networks

2020 ◽  
Author(s):  
Rubén Herzog ◽  
Arturo Morales ◽  
Soraya Mora ◽  
Joaquin Araya ◽  
María-José Escobar ◽  
...  
Keyword(s):  
Retinal Ganglion Cells ◽  
Ganglion Cells ◽  
Light Stimulus ◽  
Synthetic Data ◽  
Retinal Ganglion ◽  
Electrode Arrays ◽  
Neuronal Ensembles ◽  
Automated Method ◽  
Wide Range ◽  
Ensemble Activity

AbstractWe propose a novel, scalable, and accurate automated method for detecting neuronal ensembles from a population of spiking neurons. Our approach offers a simple yet powerful tool to study ensemble activity. It allows the participation of neurons in different ensembles, has few parameters to tune and is computationally efficient. We used spike trains of retinal ganglion cells obtained from multi-electrode array recordings under a simple ON-OFF light stimulus to test our method. We found a consistent stimuli-evoked ensemble activity intermingled with spontaneously active ensembles and irregular activity. Our results suggest that the early visual system activity is already organized in clearly distinguishable functional ensembles. To validate the performance and generality of our method, we generated synthetic data, where we found that our method accurately detects neuronal ensembles for a wide range of simulation parameters. Additionally, we found that our method outperforms current alternative methodologies. Finally, we provide a Graphic User Interface, which aims to facilitate our method’s use by the scientific community.Author summaryNeuronal ensembles are strongly interconnected groups of neurons that tend to fire together (Hebb 1949). However, even when this concept was proposed more than 70 years ago, only recent advances in multi-electrode arrays and calcium imaging, statistical methods, and computing power have made it possible to record and analyze multiple neurons’ activities spiking simultaneously, providing a unique opportunity to study how groups of neurons form ensembles spontaneously and under different stimuli scenarios. Using our method, we found that retinal ganglion cells show a consistent stimuli-evoked ensemble activity, and, when validated with synthetic data, the method shows good performance by detecting the number of ensembles, the activation times, and the core-cells for a wide range of firing rates and number of ensembles accurately.

scholarly journals Scalable and accurate method for neuronal ensemble detection in spiking neural networks

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0251647
Author(s):  
Rubén Herzog ◽  
Arturo Morales ◽  
Soraya Mora ◽  
Joaquín Araya ◽  
María-José Escobar ◽  
...  
Keyword(s):  
Ganglion Cells ◽  
Light Stimulus ◽  
Synthetic Data ◽  
Electrode Array ◽  
Accurate Method ◽  
Graphic User Interface ◽  
Population Activity ◽  
Neuronal Ensembles ◽  
Wide Range ◽  
Ensemble Activity

We propose a novel, scalable, and accurate method for detecting neuronal ensembles from a population of spiking neurons. Our approach offers a simple yet powerful tool to study ensemble activity. It relies on clustering synchronous population activity (population vectors), allows the participation of neurons in different ensembles, has few parameters to tune and is computationally efficient. To validate the performance and generality of our method, we generated synthetic data, where we found that our method accurately detects neuronal ensembles for a wide range of simulation parameters. We found that our method outperforms current alternative methodologies. We used spike trains of retinal ganglion cells obtained from multi-electrode array recordings under a simple ON-OFF light stimulus to test our method. We found a consistent stimuli-evoked ensemble activity intermingled with spontaneously active ensembles and irregular activity. Our results suggest that the early visual system activity could be organized in distinguishable functional ensembles. We provide a Graphic User Interface, which facilitates the use of our method by the scientific community.

scholarly journals Salamander retinal ganglion cell responses to rich stimuli

2020 ◽  
Author(s):  
Kolia Sadeghi ◽  
Michael J. Berry
Keyword(s):  
Ganglion Cell ◽  
Retinal Ganglion Cells ◽  
Spatial Information ◽  
Ganglion Cells ◽  
Light Stimulus ◽  
Linear Filter ◽  
Retinal Ganglion ◽  
Linear Filters ◽  
Cell Responses ◽  
Random Stimulus

AbstractThe retina’s phenomenological function is often considered to be well-understood: individual retinal ganglion cells are sensitive to a projection of the light stimulus movie onto a classical center-surround linear filter. Recent models elaborating on this basic framework by adding a second linear filter or spike histories, have been quite successful at predicting ganglion cell spikes for spatially uniform random stimuli, and for random stimuli varying spatially with low resolution. Fitting models for stimuli with more finely grained spatial variations becomes difficult because of the very high dimensionality of such stimuli. We present a method of reducing the dimensionality of a fine one dimensional random stimulus by using wavelets, allowing for several clean predictive linear filters to be found for each cell. For salamander retinal ganglion cells, we find in addition to the spike triggered average, 3 identifiable types of linear filters which modulate the firing of most cells. While some cells can be modeled fairly accurately, many cells are poorly captured, even with as many as 4 filters. The new linear filters we find shed some light on the nonlinearities in the retina’s integration of temporal and fine spatial information.

The Curved Grid Non-Illusions

2017 ◽  
Author(s):  
János Geier ◽  
Mariann Hudák
Keyword(s):  
Statistical Analysis ◽  
Retinal Ganglion Cells ◽  
Line Width ◽  
Ganglion Cells ◽  
Receptive Fields ◽  
Retinal Ganglion ◽  
Illusory Effect ◽  
Grid Line ◽  
Wide Range ◽  
Hermann Grid Illusion

The generally accepted explanation of the Hermann grid illusion is Baumgartner’s hypothesis that the illusory effect is generated by the response of retinal ganglion cells with concentric ON-OFF or OFF-ON receptive fields. To challenge this explanation, some simple distortions to the grid lines were introduced that make the illusion disappear totally, while all preconditions of Baumgartner’s hypothesis remained unchanged. Psychophysical experiments in which the distortion tolerance was measured showed the level of distortion at which the illusion disappears at a given type of distortion for a given subject. Statistical analysis shows that the distortion tolerance is independent of grid-line width within a wide range and of the type of distortion, except when one side of each line remains straight. The conclusion is the main cause of the Hermann grid illusion is the straightness of the edges of the grid lines. Similar results have been obtained in the scintillating grid.

scholarly journals Two Metabotropic γ-Aminobutyric Acid Receptors Differentially Modulate Calcium Currents in Retinal Ganglion Cells

1997 ◽  
Vol 110 (1) ◽  
pp. 45-58 ◽  
Author(s):  
Jian Zhang ◽  
Wen Shen ◽  
Malcolm M. Slaughter
Keyword(s):  
Retinal Ganglion Cells ◽  
Gaba Receptors ◽  
Gaba Receptor ◽  
Ganglion Cells ◽  
Calcium Currents ◽  
Gabab Receptors ◽  
Aminobutyric Acid ◽  
Retinal Ganglion ◽  
Wide Range ◽  
Prepulse Facilitation

Metabotropic γ-aminobutyric acid (GABA) receptors were studied in amphibian retinal ganglion cells using whole cell current and voltage clamp techniques. The aim was to identify the types of receptor present and their mechanisms of action and modulation. Previous results indicated that ganglion cells possess two ionotropic GABA receptors: GABAAR and GABACR. This study demonstrates that they also possess two types of metabotropic GABAB receptor: one sensitive to baclofen and another to cis-aminocrotonic acid (CACA). The effects of these selective agonists were blocked by GDP-β-S. Baclofen suppressed an ω-conotoxin–GVIA-sensitive barium current, and this action was reversed by prepulse facilitation, indicative of a direct G-protein pathway. The effect of baclofen was also partially occluded by agents that influence the protein kinase A (PKA) pathway. But the effect of PKA activation was unaffected by prepulse facilitation, indicating PKA acted through a parallel pathway. Calmodulin antagonists reduced the action of baclofen, whereas inhibitors of calmodulin phosphatase enhanced it. Antagonists of internal calcium release, such as heparin and ruthenium red, did not affect the baclofen response. Thus, the baclofen-sensitive receptor may respond to influx of calcium. The CACA-sensitive GABA receptor reduced current through dihydropyridine-sensitive channels. Sodium nitroprusside and 8-bromo-cGMP enhanced the action of CACA, indicating that a nitric oxide system can up-regulate this receptor pathway. CACA-sensitive and baclofen-sensitive GABAB receptors reduced spike activity in ganglion cells. Overall, retinal ganglion cells possess four types of GABA receptor, two ionotropic and two metabotropic. Each has a unique electrogenic profile, providing a wide range of neural integration at the final stage of retinal information processing.

A freely available semi-automated method for quantifying retinal ganglion cells in entire retinal flatmounts

2016 ◽  
Vol 147 ◽  
pp. 105-113 ◽  
Author(s):  
E. Geeraerts ◽  
E. Dekeyster ◽  
D. Gaublomme ◽  
M. Salinas-Navarro ◽  
L. De Groef ◽  
...  
Keyword(s):  
Retinal Ganglion Cells ◽  
Ganglion Cells ◽  
Retinal Ganglion ◽  
Automated Method

scholarly journals The Olivary Pretectal Nucleus Receives Visual Input of High Spatial Resolution

2020 ◽  
Author(s):  
Jared N. Levine ◽  
Gregory W. Schwartz
Keyword(s):  
Single Cell ◽  
Retinal Ganglion Cells ◽  
Ganglion Cells ◽  
Light Level ◽  
Single Type ◽  
Retinal Ganglion ◽  
Retinal Input ◽  
Wide Range ◽  
Pretectal Nucleus ◽  
Single Cell Type

AbstractIn the mouse, retinal output is computed by over 40 distinct types of retinal ganglion cells (RGCs) (Baden et al., 2016). Determining which of these many RGC types project to a retinorecipient region is a key step in elucidating the role that region plays in visually-mediated behaviors. Combining retrograde viral tracing and single-cell electrophysiology, we identify the RGC types which project to the olivary pretectal nucleus (OPN), a major visual structure. We find that retinal input to the OPN consists of a variety of intrinsically-photosensitive and conventional RGC types, the latter a diverse set of mostly ON RGCs. Surprisingly, while the OPN is most associated with the pupillary light reflex (PLR) pathway, requiring information about absolute luminance, we show that the majority of the retinal input to the OPN is from single cell type which transmits information unrelated to luminance. This ON-transient RGC accounts for two-thirds of the input to the OPN, and responds to small objects across a wide range of speeds. This finding suggests a role for the OPN in visually-mediated behaviors beyond the PLR.Significance statementThe olivary pretectal nucleus is a midbrain structure which receives direct input from retinal ganglion cells (RGC), and modulates pupil diameter in response to changing absolute light level. In the present study, we combine viral tracing and electrophysiology to identify the RGC types which project to the OPN. Surprisingly, the majority of its input comes from a single type which does not encode absolute luminance, but instead responds to small objects across a wide range of speeds. These findings are consistent with a role for the OPN apart from pupil control and suggest future experiments to elucidate its full role in visually-mediated behavior.

scholarly journals Studying a Light Sensor with Light: Multiphoton Imaging in the Retina

2019 ◽  
Author(s):  
Thomas Euler ◽  
Katrin Franke ◽  
Tom Baden
Keyword(s):  
Retinal Ganglion Cells ◽  
Neuronal Activity ◽  
Ganglion Cells ◽  
Light Stimulus ◽  
Retinal Ganglion ◽  
Multiphoton Imaging ◽  
Vertebrate Retina ◽  
Two Photon ◽  
All Optical ◽  
The Brain

Two-photon imaging of light stimulus-evoked neuronal activity has been used to study all neuron classes in the vertebrate retina, from the photoreceptors to the retinal ganglion cells. Clearly, the ability to study retinal circuits down to the level of single synapses or zoomed out at the level of complete populations of neurons, has been a major asset in our understanding of this beautiful circuit. In this chapter, we discuss the possibilities and pitfalls of using an all-optical approach in this highly light-sensitive part of the brain.

scholarly journals Voltage-gated calcium channel subunit α2δ-3 shapes light responses of mouse retinal ganglion cells mainly in low and moderate light levels

2020 ◽  
Author(s):  
Hartwig Seitter ◽  
Vithiyanjali Sothilingam ◽  
Boris Benkner ◽  
Marina Garcia Garrido ◽  
Alexandra Kling ◽  
...  
Keyword(s):  
Calcium Channels ◽  
Retinal Ganglion Cells ◽  
Ganglion Cells ◽  
Horizontal Cell ◽  
Gaussian White Noise ◽  
Retinal Ganglion ◽  
Visual Responses ◽  
Electrode Arrays ◽  
Voltage Gated ◽  
Voltage Gated Calcium Channels

AbstractLittle is known about the function of the auxiliary α2δ subunits of voltage-gated calcium channels in the retina. We investigated the role of α2δ-3 (Cacna2d3) using a mouse in which α2δ-3 was knocked out by LacZ insertion. Behavior experiments indicated a normal optokinetic reflex in α2δ-3 knockout animals. Strong expression of α2δ-3 could be localized to horizontal cells using the LacZ-reporter, but horizontal cell mosaic and currents carried by horizontal cell voltage-gated calcium channels were unchanged by the α2δ-3 knockout. In vivo electroretinography revealed unaffected photoreceptor activity and signal transmission to depolarizing bipolar cells. We recorded visual responses of retinal ganglion cells with multi-electrode arrays in scotopic to photopic luminance levels and found subtle changes in α2δ-3 knockout retinas. Spontaneous activity in OFF ganglion cells was elevated in all luminance levels. Differential response strength to high- and low-contrast Gaussian white noise was compressed in ON ganglion cells during mesopic ambient luminance and in OFF ganglion cells during scotopic and mesopic ambient luminances. In a subset of ON ganglion cells, we found a sharp increase in baseline spiking after the presentation of drifting gratings in scotopic luminance. This increase happened after gratings of different spatial properties in knockout compared to wild type retinas. In a subset of ON ganglion cells of the α2δ-3 knockout, we found altered delays in rebound-like spiking to full-field contrast steps in scotopic luminance. In conclusion, α2δ-3 seems to participate in shaping visual responses mostly within brightness regimes when rods or both rods and cones are active.

Calcium-Activated Potassium Conductances in Retinal Ganglion Cells of the Ferret

1998 ◽  
Vol 79 (1) ◽  
pp. 151-158 ◽  
Author(s):  
Guo-Yong Wang ◽  
David W. Robinson ◽  
Leo M. Chalupa
Keyword(s):  
Potassium Channels ◽  
Potassium Channel ◽  
Retinal Ganglion Cells ◽  
Ganglion Cells ◽  
Membrane Properties ◽  
Retinal Ganglion ◽  
Wide Range ◽  
Potassium Conductances ◽  
Calcium Activated Potassium Channels ◽  
Calcium Activated Potassium Channel

Wang, Guo-Yong, David W. Robinson, and Leo M. Chalupa. Calcium-activated potassium conductances in retinal ganglion cells of the ferret. J. Neurophysiol. 79: 151–158, 1998. Patch-clamp recordings were made from isolated and intact retinal ganglion cells (RGCs) of the ferret to examine the calcium-activated potassium channels expressed by these neurons and to determine their functional role in the generation of spikes and spiking patterns. Single-channel recordings from isolated neurons revealed the presence of two calcium-sensitive potassium channels that had conductances of 118 and 22 pS. The properties of these two channels were shown to be similar to those ascribed to the large-conductance calcium-activated potassium channel (BKCa) and small-conductance calcium-activated potassium channel (SKCa) channels in other neurons. Whole cell recordings from isolated RGCs showed that apamin and charybdotoxin (CTX), specific blockers of the SKCa and BKCa channels, respectively, resulted in a shortening of the time to threshold and a reduction in the hyperpolarization after the spike. Addition of these blockers also resulted in a significant increase in spike frequency over a wide range of maintained depolarizations. Similar effects of apamin and CTX were observed during current-clamp recordings from intact alpha and beta ganglion cells, morphologically identified after Lucifer yellow filling. About 20% of these neurons did not exhibit a sensitivity to either blocker, suggesting the presence of functionally distinct subgroups of alpha and beta RGCs on the basis of their intrinsic membrane properties. The expression of these calcium-activated potassium channels in the majority of alpha and beta cells provides a means by which the activity of these output neurons could be modulated by retinal neurochemicals.

scholarly journals Modeling a population of retinal ganglion cells with restricted Boltzmann machines

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Riccardo Volpi ◽  
Matteo Zanotto ◽  
Alessandro Maccione ◽  
Stefano Di Marco ◽  
Luca Berdondini ◽  
...  
Keyword(s):  
Retinal Ganglion Cells ◽  
Latent Variables ◽  
Latent Variable ◽  
Ganglion Cells ◽  
Visual Stimuli ◽  
Retinal Ganglion ◽  
Electrode Arrays ◽  
Restricted Boltzmann Machines ◽  
Boltzmann Machines ◽  
Spiking Activity

Abstract The retina is a complex circuit of the central nervous system whose aim is to encode visual stimuli prior the higher order processing performed in the visual cortex. Due to the importance of its role, modeling the retina to advance in interpreting its spiking activity output is a well studied problem. In particular, it has been shown that latent variable models can be used to model the joint distribution of Retinal Ganglion Cells (RGCs). In this work, we validate the applicability of Restricted Boltzmann Machines to model the spiking activity responses of a large a population of RGCs recorded with high-resolution electrode arrays. In particular, we show that latent variables can encode modes in the RGC activity distribution that are closely related to the visual stimuli. In contrast to previous work, we further validate our findings by comparing results associated with recordings from retinas under normal and altered encoding conditions obtained by pharmacological manipulation. In these conditions, we observe that the model reflects well-known physiological behaviors of the retina. Finally, we show that we can also discover temporal patterns, associated with distinct dynamics of the stimuli.

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