Fabian Kloosterman

Fabian Kloosterman
Neuro-Electronics Research Flanders | NERF

PhD

About

59
Publications
11,055
Reads
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2,193
Citations
Additional affiliations
October 2011 - present
Neuro-Electronics Research Flanders
Position
  • Principal Investigator
May 2003 - September 2011
Massachusetts Institute of Technology
Position
  • PostDoc Position
September 1998 - December 2002
University of Amsterdam
Position
  • PhD Student

Publications

Publications (59)
Article
Hippocampal sharp-wave ripple activity (SWRs) and the associated replay of neural activity patterns are well-known for their role in memory consolidation. This activity has been studied using electrophysiological approaches, as high temporal resolution is required to recognize SWRs in the neuronal signals. However, it has been difficult to analyze...
Article
Reward value is known to modulate learning speed in spatial memory tasks, but little is known about its influence on the dynamical changes in hippocampal spatial representations. Here, we monitored the trial-to-trial changes in hippocampal place cell activity during the acquisition of place-reward associations with varying reward size. We show a fa...
Article
Objective: Spike sorting is the process of extracting neuronal action potentials, or spikes, from an extracellular brain recording, and assigning each spike to its putative source neuron. Spike sorting is usually treated as a clustering problem. However, this clustering process is known to be affected by overlapping spikes. Existing methods for re...
Article
How dynamic activity in neural circuits gives rise to behavior is a major area of interest in neuroscience. A key experimental approach for addressing this question involves measuring extracellular neuronal activity in awake, behaving animals. Recently developed Neuropixels probes have provided a step change in recording neural activity in large ti...
Article
Recording many neurons for a long time The ultimate aim of chronic recordings is to sample from the same neuron over days and weeks. However, this goal has been difficult to achieve for large populations of neurons. Steinmetz et al. describe the development and testing of Neuropixels 2.0. This new electrophysiological recording tool is a miniaturiz...
Article
Full-text available
Spike sorting is the process of retrieving the spike times of individual neurons that are present in an extracellular neural recording. Over the last decades, many spike sorting algorithms have been published. In an effort to guide a user towards a specific spike sorting algorithm, given a specific recording setting (i.e., brain region and recordin...
Preprint
Full-text available
Reward value is known to modulate learning speed in spatial memory tasks, but little is known about its influence on the dynamical changes in hippocampal spatial representations. Here, we monitored the trial-to-trial changes in hippocampal place cell activity during the acquisition of place-reward associations with varying reward size. We show a fa...
Article
Full-text available
Memories of past events and common knowledge are critical to flexibly adjust one's future behavior based on prior experiences. The formation and the transformation of these memories into a long-lasting form are supported by a dialogue between populations of neurons in the cortex and the hippocampus. Not all experiences are remembered equally well o...
Preprint
Full-text available
Memories of past events and common knowledge are critical to flexibly adjust one's future behavior based on prior experiences. The formation and the transformation of these memories into a long-lasting form are supported by a dialog between the coordinated activity of population of neurons in the cortex and the hippocampus. Not all experiences are...
Article
In this paper, we propose three novel linear filter design methods for use in a multi-pattern recognition task with overlapping patterns and strong peak interferers. The recognition is based on a linear filter-and-threshold approach, which is particularly interesting when the task has to be performed in a computationally constrained environment. Th...
Article
Full-text available
Objective: Long-term electrophysiological recordings of neural activity in freely behaving animals are indispensable to advance the understanding of complex brain function. It is a technical challenge to chronically monitor the detailed activity across multiple distributed brain regions in freely behaving animals over a period of months. Here we p...
Preprint
Spike sorting is the process of retrieving the spike times of individual neurons that are present in an extracellular neural recording. Over the last decades, many spike sorting algorithms have been published. In an effort to guide a user towards a specific spike sorting algorithm, given a specific recording setting (i.e., brain region and recordin...
Conference Paper
Spike sorting is the process of assigning neural spikes in an extracellular brain recording to their putative neurons. Optimal pre-whitened template matching filters that are used in spike sorting typically suffer from ill-conditioning. In this paper, we investigate the origin of this ill-conditioning and the way in which it influences the resultin...
Article
Offline replay of hippocampal neural patterns supports the acquisition of new tasks in novel contexts, but its contribution to consolidation of salient experiences in a familiar context is unknown. Here, we show that in a highly familiar spatial memory task, large rewards selectively enhanced performance for demanding task configurations. The rewar...
Article
Full-text available
Uncovering spatial representations from large-scale ensemble spike activity in specific brain circuits provides valuable feedback in closed-loop experiments. We develop a graphics processing unit (GPU)-powered population-decoding system for ultrafast reconstruction of spatial positions from rodents’ unsorted spatiotemporal spiking patterns, during...
Article
Full-text available
Communication in neural circuits across the cortex is thought to be mediated by spontaneous temporally organized patterns of population activity lasting ~50 –200 ms. Closed-loop manipulations have the unique power to reveal direct and causal links between such patterns and their contribution to cognition. Current brain–computer interfaces, however,...
Article
Objective: The process of grouping neuronal spikes in an extracellular recording according to their neuronal sources, is generally referred to as spike sorting. Currently, the use of spike sorting is mainly limited to an offline usage, where spikes are sorted after the data acquisition has been completed. In this paper, we propose a discriminative...
Article
High-density electrode arrays used to read out neural activity will soon surpass the limits of the amount of data that can be transferred within reasonable energy budgets. This is true for wired brain implants when the required bandwidth becomes very high, and even more so for untethered brain implants that require wireless transmission of data. We...
Article
For the sake of rigorous control of task variables, hippocampal place cells have been usually studied in relatively simple environments. To approach the situation of real-life navigation in an urban-like environment, we recorded CA1 place cells while rats performance a memory task in a ‘Townmaze' with two start locations, three alternate paths in t...
Article
Full-text available
We present a high electrode density and high channel count CMOS (complementary metal-oxide-semiconductor) active neural probe containing 1344 neuron sized recording pixels (20 µm × 20 µm) and 12 reference pixels (20 µm × 80 µm), densely packed on a 50 µm thick, 100 µm wide, and 8 mm long shank. The active electrodes or pixels consist of dedicated i...
Article
Full-text available
See Lenck-Santini (doi:10.1093/awx205) for a scientific commentary on this article. Epileptic seizures represent altered neuronal network dynamics, but the temporal evolution and cellular substrates of the neuronal activity patterns associated with spontaneous seizures are not fully understood. We used simultaneous recordings from multiple neurons...
Article
Full-text available
Epileptic seizures represent altered neuronal network dynamics, but the temporal evolution and cellular substrates of the neuronal activity patterns associated with spontaneous seizures are not fully understood. We used simultaneous recordings from multiple neurons in the hippocampus and neocortex of rats with chronic temporal lobe epilepsy to demo...
Article
Full-text available
Objective: Closed-loop experiments provide unique insights into brain dynamics and function. Here, we demonstrate an open-source software platform that enables high-performance real-time processing of streaming experimental data, suitable for a wide range of closed-loop experiments. Approach: We wrote a C++ multi-threaded software (Falcon) in wh...
Conference Paper
We present a high density CMOS neural probe with active electrodes (pixels), consisting of dedicated in-situ circuits for signal source amplification. The complete probe contains 1356 neuron sized (20×20 μm<sup>2</sup>) pixels densely packed on a 50 μm thick, 100 μm wide and 8 mm long shank. It allows simultaneous high-performance recording from 67...
Article
Full-text available
Objective: Understanding how neuronal assemblies underlie cognitive function is a fundamental question in system neuroscience. It poses the technical challenge to monitor the activity of populations of neurons, potentially widely separated, in relation to behaviour. In this paper, we present a new system which aims at simultaneously recording from...
Article
Pyramidal neurons recorded from the rat hippocampus and entorhinal cortex, such as place and grid cells, have diverse receptive fields, which are either unimodal or multimodal. Spiking activity from these cells encodes information about the spatial position of freely foraging rat. At fine timescales, a neuron's spike activity also depends significa...
Article
Full-text available
To gain better understanding of how neural ensembles communicate and process information, neuroscientists require neural decoding tools to extract information embedded in neurons’ spiking activities. Bayesian decoding is one of the neural population decoding approaches that is able to extract information directly from the ensemble spiking activity,...
Article
This paper describes a low power closed-loop compressive sensing (CS) based neural recording system. This system provides an efficient method to reduce data transmission bandwidth for implantable neural recording devices. By doing so, this technique reduces a majority of system power consumption which is dissipated at data readout interface. The de...
Chapter
Background: In the neocortex, information is represented by patterns of spike activity occurring over populations of neurons. A fundamental task in neuroscience is to understand how the information is encoded and transmitted in neural population activity. In comparison with the single unit activity, population activity is more information rich and...
Article
Acknowledgements O'Neill, J., Pleydell-Bouverie, B., Dupret, D., and Csicsvari J. (2010). Play it again: reactivation of waking experience and memory. Trends Neurosci. 33(5):220-9. doi: 10.1016/j.tins.2010.01.006. Kloosterman, F. (2012). "Analysis of Hippocampal Memory Replay Using Neural Population Decoding" in Neuronal Network Analysis. Neuromet...
Article
Spatial learning requires the hippocampus, and the replay of spatial sequences during hippocampal sharp wave-ripple (SPW-R) events of quiet wakefulness and sleep is believed to play a crucial role. To test whether the coordination of VTA reward prediction error signals with these replayed spatial sequences could contribute to this process, we recor...
Article
The past decade has witnessed an explosive growth in our ability to observe and measure brain activity. Among different functional brain imaging techniques, the electrical measurement of neural activity using neural probes provides highest temporal resolution. Yet, the electrode density and the observability of currently available neural probe tech...
Article
Full-text available
A fundamental task in neuroscience is to understand how neural ensembles represent information. Population decoding is a useful tool to extract information from neuronal populations based on the ensemble spiking activity. We propose a novel Bayesian decoding paradigm to decode unsorted spikes in the rat hippocampus. Our approach uses a direct mappi...
Article
Full-text available
Neural decoding is an important approach for extracting information from population codes. We previously proposed a novel transductive neural decoding paradigm and applied it to reconstruct the rat's position during navigation based on unsorted rat hippocampal ensemble spiking activity. Here, we investigate several important technical issues of thi...
Article
Full-text available
Hippocampal population codes play an important role in representation of spatial environment and spatial navigation. Uncovering the internal representation of hippocampal population codes will help understand neural mechanisms of the hippocampus. For instance, uncovering the patterns represented by rat hippocampus (CA1) pyramidal cells during perio...
Chapter
Large-scale recording of neural activity in waking animals provides us with a window on computations performed in the brain during behavior. In order to better understand these computations, population decoding techniques are used to study what information about the external environment is represented by neural ensemble activity. Decoding approache...
Conference Paper
Full-text available
Point process generalized linear models (GLMs) have been widely used for neural spike trains analysis. Statistical inference for GLMs include maximum likelihood and Bayesian estimation. Variational Bayesian (VB) methods provide a computationally appealing means to infer the posterior density of unknown parameters, in which conjugate priors are desi...
Article
During pauses in exploration, ensembles of place cells in the rat hippocampus re-express firing sequences corresponding to recent spatial experience. Such "replay" co-occurs with ripple events: short-lasting (approximately 50-120 ms), high-frequency (approximately 200 Hz) oscillations that are associated with increased hippocampal-cortical communic...
Article
Full-text available
Chronic recording of large populations of neurons is a valuable technique for studying the function of neuronal circuits in awake behaving rats. Lightweight recording devices carrying a high density array of tetrodes allow for the simultaneous monitoring of the activity of tens to hundreds of individual neurons. Here we describe a protocol for the...
Article
Full-text available
The tetrode, a bundle of four electrodes, has proven to be a valuable tool for the simultaneous recording of multiple neurons in-vivo. The differential amplitude of action potential signatures over the channels of a tetrode allows for the isolation of single-unit activity from multi-unit signals. The ability to precisely control the stereotaxic loc...
Article
Full-text available
Fast oscillations or "ripples" are found in the local field potential (LFP) of the rodent hippocampus during awake and sleep states. Ripples have been found to correlate with memory related neural processing, however, the functional role of the ripple has yet to be fully established. We applied a Kalman smoother based estimator of instantaneous fre...
Article
Full-text available
Spatially-modulated firing of hippocampal 'place cells' is thought to subserve spatial learning in the rat. Ensemble recordings have shown that these cells re-express behavio-ral firing sequences during sleep. Recently, replay of the reverse of behavioral sequences has been reported in the awake rat at reward sites. These phenomena are hypothesized...
Article
Full-text available
We tested the hypothesis that presynaptic GABA(B) receptors on glutamatergic terminals (GABA(B) heterosynaptic receptors) decreased in efficacy after partial hippocampal kindling. Rats were implanted with chronically indwelling electrodes and 15 hippocampal afterdischarges were evoked by high-frequency electrical stimulation of hippocampal CA1. Con...
Article
The characteristic cell loss in layer III of the medial entorhinal area (MEA-III) in human mesial temporal lobe epilepsy is reproduced in the rat kainate model of the disease. To understand how this cell loss affects the functional properties of the MEA, we investigated whether projections from the presubiculum (prS), providing a main input to the...
Article
We investigated whether the functional network properties of the medial entorhinal area (MEA) of the entorhinal cortex were altered in a rat model of chronic epilepsy that is characterized by extensive cell loss in MEA layer III. Responses were evoked in the entorhinal cortex by electrical stimulation of the subiculum in anesthetized chronic epilep...
Article
The entorhinal cortex has long been recognized as an important interface between the hippocampal formation and the neocortex. The notion of bidirectional connections between the entorhinal cortex and the hippocampal formation have led to the suggestion that hippocampal output originating in CA1 and subiculum may reenter hippocampal subfields via th...
Article
The hippocampal formation communicates with the neocortex mainly through the adjacent entorhinal cortex. Neurons projecting to the hippocampal formation are found in the superficial layers of the entorhinal cortex and are largely segregated from the neurons receiving hippocampal output, which are located in deep entorhinal layers. We studied the co...
Article
In this study, we analyzed in detail the topographic organization of the subiculoparahippocampal projection in the rat. The anterograde tracers Phaseolus vulgaris leucoagglutinin-L and biotinylated dextran amine were injected into the subiculum at different septotemporal and transverse levels. Deep layers of the ento-, peri-, and postrhinal cortice...
Article
Full-text available
This protocol describes an implementation of recording and analysis of evoked potentials in the hippocampal cortex, combined with lesioning using multichannel silicon probes. Multichannel recording offers the advantage of capturing a potential field at one instant in time. The potentials are then subjected to current source density (CSD) analysis,...
Article
Full-text available
There is controversy concerning whether orthodromic action potentials originate from the apical or basal dendrites of CA1 pyramidal cells in vivo. The participation of the dendrites in the initialization and propagation of population spikes in CA1 of urethan-anesthetized rats in vivo was studied using simultaneously recorded field potentials and cu...
Article
Evoked field potentials and current-source-density analysis were used to study the olfactory, entorhinal, and perirhinal projections to the hippocampus. In urethane-anesthetized rats, various structures were electrically stimulated, and evoked potentials were mapped using glass micropipettes or multichannel silicon probes. Stimulation of the olfact...
Chapter
Electric activity plays a major role in the fine-tuning of neuronal connections during development. Since alterations in connectivity will in turn affect network activity it is clear that neuronal network formation is the result of reciprocal interactions between the activity and the structure of the network. To investigate the role of electric act...
Article
The subiculum has long been considered as a simple bidirectional relay region interposed between the hippocampus and the temporal cortex. Recent evidence, however, suggests that this region has specific roles in the cognitive functions and pathological deficits of the hippocampal formation. A group of 20 researchers participated in an ESF-sponsored...

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Projects (5)
Project
Study the impact of various aspects of experience, such as reward or emotion, on memory processes