A method for closed-loop presentation of sensory stimuli conditional on the internal brain-state of awake animals.

Abstract:

:Brain activity often consists of interactions between internal-or on-going-and external-or sensory-activity streams, resulting in complex, distributed patterns of neural activity. Investigation of such interactions could benefit from closed-loop experimental protocols in which one stream can be controlled depending on the state of the other. We describe here methods to present rapid and precisely timed visual stimuli to awake animals, conditional on features of the animal's on-going brain state; those features are the presence, power and phase of oscillations in local field potentials (LFP). The system can process up to 64 channels in real time. We quantified its performance using simulations, synthetic data and animal experiments (chronic recordings in the dorsal cortex of awake turtles). The delay from detection of an oscillation to the onset of a visual stimulus on an LCD screen was 47.5ms and visual-stimulus onset could be locked to the phase of ongoing oscillations at any frequency ≤40Hz. Our software's architecture is flexible, allowing on-the-fly modifications by experimenters and the addition of new closed-loop control and analysis components through plugins. The source code of our system "StimOMatic" is available freely as open-source.

journal_name

J Neurosci Methods

authors

Rutishauser U,Kotowicz A,Laurent G

doi

10.1016/j.jneumeth.2013.02.020

subject

Has Abstract

pub_date

2013-04-30 00:00:00

pages

139-55

issue

1

eissn

0165-0270

issn

1872-678X

pii

S0165-0270(13)00094-0

journal_volume

215

pub_type

杂志文章
  • Overexpression of growth-associated proteins in the neurons of adult transgenic mice.

    abstract::The Thy-1.2 expression cassette described in this report drives strong constitutive expression of transgenes specifically in the neurons of adult transgenic mice. Transgene expression begins at P6-10, at a time when it can affect activity-dependent rearrangements of synaptic connections and neuron-glia interactions du...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章,评审

    doi:10.1016/s0165-0270(96)00121-5

    authors: Caroni P

    更新日期:1997-01-01 00:00:00

  • Randomising stimulus intensity improves the variability and reliability of the assessment of corticospinal excitability.

    abstract:BACKGROUND:Advances in the control of transcranial magnetic stimulation (TMS) have enabled greater randomisation of stimulus intensity. It is unclear if such randomisation improves assessments of corticospinal excitability. NEW METHOD:We recorded the amplitude of TMS-induced motor evoked potentials (MEPs) from the fir...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2020.108813

    authors: Suckley JJ,Waters TJ,Tran M,Stapley PJ,Shemmell J,Walsh JA,McAndrew DJ

    更新日期:2020-08-01 00:00:00

  • A method demonstrating motor endplates for light and electron microscopy.

    abstract::The cytochemical localization of acetylcholinesterase activity at motor endplates is commonly employed prior to electron microscopic examination. Methods which involve the use of thiocholine esters often lead to a loss of resolution due to the spread to surrounding tissues of an extremely dense reaction product. A met...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(82)90031-0

    authors: Strum JM,Hall-Craggs EC

    更新日期:1982-11-01 00:00:00

  • Automatic analysis of cortical signals recorded with voltage-sensitive dyes using a forward-backward non-linear filtering technique and deconvolution.

    abstract::A method for automatically analyzing cortical signals recorded with voltage-sensitive dyes and a photodiode array is described. First, a forward-backward non-linear filtering technique is used to eliminate the background noise and preserve the fast transients of the signals. Then the filtered signals are deconvoluted ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(95)00105-0

    authors: Litaudon P,Girardeau-Montaut C,Girardeau-Montaut JP,Cattarelli M

    更新日期:1995-12-01 00:00:00

  • A transgenic rat expressing green fluorescent protein (GFP) in peripheral nerves provides a new hindlimb model for the study of nerve injury and regeneration.

    abstract:BACKGROUND:In order to evaluate nerve regeneration in clinically relevant hindlimb surgical paradigms not feasible in fluorescent mice models, we developed a rat that expresses green fluorescent protein (GFP) in neural tissue. METHODS:Transgenic Sprague-Dawley rat lines were created using pronuclear injection of a tra...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2011.10.011

    authors: Moore AM,Borschel GH,Santosa KB,Flagg ER,Tong AY,Kasukurthi R,Newton P,Yan Y,Hunter DA,Johnson PJ,Mackinnon SE

    更新日期:2012-02-15 00:00:00

  • Construction of simple, customised, brain-spanning, multi-channel, linear microelectrode arrays.

    abstract:BACKGROUND:The construction of multichannel micro-electrode arrays (MEA) generally requires complex and expensive procedures. Here we describe a simple, cheap, flexible method of linear MEA construction. NEW METHOD:Our method allows manufacture of linear MEA (cross section ∼ 375 × 250 μm with 12 electrodes) of any des...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2020.109011

    authors: Banstola A,Silva C,Ulrich K,Ruan M,Robertson L,McNaughton N

    更新日期:2021-01-15 00:00:00

  • A perfused in vitro preparation of hypothalamus for electrophysiological studies on neurosecretory neurons.

    abstract::A technique for the preparation and recording of mammalian supraoptic nucleus neurosecretory neurons maintained in vitro through perfusion of the anterior cerebral artery is described. A slice of basal diencephalon measuring approximately 8 X 8 X 2 mm that includes the pituitary stalk and medial preoptic-anterior peri...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(83)90002-x

    authors: Bourque CW,Renaud LP

    更新日期:1983-03-01 00:00:00

  • Common spatial pattern and wavelet decomposition for motor imagery EEG- fTCD brain-computer interface.

    abstract:BACKGROUND:Recently, hybrid brain-computer interfaces (BCIs) combining more than one modality have been investigated with the aim of boosting the performance of the existing single-modal BCIs in terms of accuracy and information transfer rate (ITR). Previously, we introduced a novel hybrid BCI in which EEG and fTCD mod...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2019.03.018

    authors: Khalaf A,Sejdic E,Akcakaya M

    更新日期:2019-05-15 00:00:00

  • Isolation and culture of primary embryonic zebrafish neural tissue.

    abstract:BACKGROUND:Primary cell culture is a valuable tool to utilize in parallel with in vivo studies in order to maximize our understanding of the mechanisms surrounding neurogenesis and central nervous system (CNS) regeneration and plasticity. The zebrafish is an important model for biomedical research and primary neural ce...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2019.108419

    authors: Patel BB,Clark KL,Kozik EM,Dash L,Kuhlman JA,Sakaguchi DS

    更新日期:2019-12-01 00:00:00

  • Localising and classifying neurons from high density MEA recordings.

    abstract::Neuronal microcircuits are formed of a myriad of spatially and functionally specific cell classes. Despite the importance of the spatial component in the characterisation of neural circuits, it has not received the attention it deserves. While multi-electrodes are widely used in the study of microcircuits, the spatial...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2014.05.037

    authors: Delgado Ruz I,Schultz SR

    更新日期:2014-08-15 00:00:00

  • Voltage-sensitive dye recording using retrogradely transported dye in the chicken spinal cord: staining and signal characteristics.

    abstract::We describe a novel method for retrogradely labeling specific neuronal populations using voltage-sensitive dyes. Styryl dyes were injected into the ventral roots of the isolated embryonic chick spinal cord. After waiting several hours, the dye labeled motoneurons and autonomic preganglionic neurons. Neuronal cell bodi...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(96)00108-2

    authors: Wenner P,Tsau Y,Cohen LB,O'Donovan MJ,Dan Y

    更新日期:1996-12-28 00:00:00

  • Random forest feature selection, fusion and ensemble strategy: Combining multiple morphological MRI measures to discriminate among healhy elderly, MCI, cMCI and alzheimer's disease patients: From the alzheimer's disease neuroimaging initiative (ADNI) data

    abstract:BACKGROUND:In the era of computer-assisted diagnostic tools for various brain diseases, Alzheimer's disease (AD) covers a large percentage of neuroimaging research, with the main scope being its use in daily practice. However, there has been no study attempting to simultaneously discriminate among Healthy Controls (HC)...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2017.12.010

    authors: Dimitriadis SI,Liparas D,Tsolaki MN,Alzheimer's Disease Neuroimaging Initiative.

    更新日期:2018-05-15 00:00:00

  • A miniaturized chronic microelectrode drive for awake behaving head restrained mice and rats.

    abstract::The present work introduces an electrode microdrive system small enough to be placed into two distinct brain areas in head-fixed mice. To meet the space constraint imposed by the size of mice and the additional presence of a head post, the size and weight of the components were minimized. In the current version, an in...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2009.12.015

    authors: Haiss F,Butovas S,Schwarz C

    更新日期:2010-03-15 00:00:00

  • A novel device for studying weight supported, quadrupedal overground locomotion in spinal cord injured rats.

    abstract:BACKGROUND:Providing weight support facilitates locomotion in spinal cord injured animals. To control weight support, robotic systems have been developed for treadmill stepping and more recently for overground walking. NEW METHOD:We developed a novel device, the body weight supported ambulatory rodent trainer (i.e. BA...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2015.03.015

    authors: Hamlin M,Traughber T Jr,Reinkensmeyer DJ,de Leon RD

    更新日期:2015-05-15 00:00:00

  • A lucite plate method for 3-dimensional reconstruction of neuronal populations.

    abstract::A Lucite plate reconstruction method is described which, when combined with HRP histochemistry, provides an excellent means of visualizing, in 3-dimensional fashion, the functional organization of neuronal populations. Color photomicrographs of representative serial sections were made through the baboon oculomotor nuc...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(81)90019-4

    authors: Augustine JR

    更新日期:1981-06-01 00:00:00

  • Increased throughput assays of locomotor dysfunction in Drosophila larvae.

    abstract::Larval locomotion is a sensitive readout of a range of nervous system deficits in Drosophila, and has been utilised to quantify modulation of the disease phenotype in models of human disease. Single larvae are typically analysed in series using manual quantification of parameters such as contraction rate, or grouped t...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2011.08.037

    authors: Sinadinos C,Cowan CM,Wyttenbach A,Mudher A

    更新日期:2012-01-30 00:00:00

  • Improved method to track and precisely count Schwann cells post-transplantation in a peripheral nerve injury model.

    abstract:BACKGROUND:To optimize survival evaluation of Schwann cells (SCs) in vivo, we tested fluorescent labeling of the nucleus as an improved method of tracking and counting the transplanted SCs at sciatic nerve injury sites in rodents. We also investigated if co-administering cells with the glial growth factor Neuregulin-1 ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2016.08.009

    authors: Gambhir HS,Raharjo E,Forden J,Kumar R,Mishra C,Guo GF,Grochmal J,Shapira Y,Midha R

    更新日期:2016-11-01 00:00:00

  • A horizontal slice preparation for examining the functional connectivity of dorsal column fibres in mouse spinal cord.

    abstract::In spinal cord injury (SCI) research, axon regeneration across spinal lesions is most often assessed using anatomical methods. It would be extremely advantageous, however, to examine the functional synaptic connectivity of regenerating fibres, using high-resolution electrophysiological methods. We have therefore devel...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2011.06.017

    authors: Flynn JR,Brichta AM,Galea MP,Callister RJ,Graham BA

    更新日期:2011-09-15 00:00:00

  • Assessment of executive function in adolescence: a comparison of traditional and virtual reality tools.

    abstract::Paper-pencil type tests are traditionally used in the assessment of executive functions (EF); however, concerns have been raised as to whether these represent actual functioning in everyday life. Virtual reality (VR) environments offer a novel alternative for the assessment of cognitive function and therefore have the...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2013.07.005

    authors: Lalonde G,Henry M,Drouin-Germain A,Nolin P,Beauchamp MH

    更新日期:2013-09-30 00:00:00

  • Properties of the new fluorescent Na+ indicator CoroNa Green: comparison with SBFI and confocal Na+ imaging.

    abstract::Neuronal activity causes substantial Na+ transients in fine cellular processes such as dendrites and spines. The physiological consequences of such Na+ transients are still largely unknown. High-resolution Na+ imaging is pivotal to study these questions, and, up to now, two-photon imaging with the fluorescent Na+ indi...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2006.01.009

    authors: Meier SD,Kovalchuk Y,Rose CR

    更新日期:2006-09-15 00:00:00

  • The role of diversity in complex ICA algorithms for fMRI analysis.

    abstract:BACKGROUND:The widespread use of data-driven methods, such as independent component analysis (ICA), for the analysis of functional magnetic resonance imaging data (fMRI) has enabled deeper understanding of neural function. However, most popular ICA algorithms for fMRI analysis make several simplifying assumptions, thus...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2016.03.012

    authors: Du W,Levin-Schwartz Y,Fu GS,Ma S,Calhoun VD,Adalı T

    更新日期:2016-05-01 00:00:00

  • Custom-fit radiolucent cranial implants for neurophysiological recording and stimulation.

    abstract:BACKGROUND:Recording and manipulating neural activity in awake behaving animal models requires long-term implantation of cranial implants that must address a variety of design considerations, which include preventing infection, minimizing tissue damage, mechanical strength of the implant, and MRI compatibility. NEW ME...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2014.12.011

    authors: Mulliken GH,Bichot NP,Ghadooshahy A,Sharma J,Kornblith S,Philcock M,Desimone R

    更新日期:2015-02-15 00:00:00

  • Comparative one- and two-photon uncaging of MNI-glutamate and MNI-kainate on hippocampal CA1 neurons.

    abstract:BACKGROUND:The light-induced release of neurotransmitters from caging chromophores provides a powerful means to study the underlying receptors in a physiologically relevant context. Surprisingly, most caged neurotransmitters, including the widely used 4-methoxy-7-nitroindolinyl (MNI)-glutamate, show strong antagonism a...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2017.10.013

    authors: Passlick S,Ellis-Davies GCR

    更新日期:2018-01-01 00:00:00

  • Test-retest reliability of paired pulse suppression paradigm using auditory change-related response.

    abstract:BACKGROUND:Sensory suppression is an important brain function for appropriate processing of information and is known to be impaired in patients with various types of mental illness. Long latency suppression which is a paradigm using change-related cortical response with repeated paired pulses embedded in a train of con...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2021.109087

    authors: Takeuchi N,Fujita K,Kinukawa T,Sugiyama S,Kanemoto K,Nishihara M,Inui K

    更新日期:2021-01-25 00:00:00

  • A simple electronic unit allowing extracellular recording and stimulation through the same wire hook or suction electrode.

    abstract::A simple and easily constructed unit was designed using a buffer amplifier, a programmable transconductance amplifier and an active filter. The unit allows extracellular recording and stimulation through the same electrode. Thus in experiments where it is required to stimulate a nerve and record the effects of the sti...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(84)90034-7

    authors: Hatzopoulos A,Theophilidis G

    更新日期:1984-08-01 00:00:00

  • Responses of rats to noxious mechanical stimulation of their tails during tail reperfusion following transient ischaemia.

    abstract::We investigated whether conscious rats exhibit hyperalgesia to noxious mechanical stimuli during tail reperfusion following transient tail ischaemia. Mechanical stimuli were delivered by three mechanical algometers, differing in contact area, geometry and rate of application. Tail ischaemia was induced by applying a p...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(00)00313-7

    authors: Vidulich L,Mitchell D

    更新日期:2000-11-30 00:00:00

  • A semi-in-vivo preparation for optical recording of the insect brain.

    abstract::We describe a method for optically recording neuronal activity from an intact insect brain, upon natural sensory stimulation. In this preparation, the head capsule of the honeybee, Apis mellifera, is isolated from the body while leaving the entire brain undamaged. In short, a hole is first cut into the cuticule to all...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(97)00080-0

    authors: Galizia CG,Joerges J,Küttner A,Faber T,Menzel R

    更新日期:1997-09-05 00:00:00

  • A mobile, high-throughput semi-automated system for testing cognition in large non-primate animal models of Huntington disease.

    abstract:BACKGROUND:For reasons of cost and ethical concerns, models of neurodegenerative disorders such as Huntington disease (HD) are currently being developed in farm animals, as an alternative to non-human primates. Developing reliable methods of testing cognitive function is essential to determining the usefulness of such ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2015.08.025

    authors: McBride SD,Perentos N,Morton AJ

    更新日期:2016-05-30 00:00:00

  • The effects of physiologically plausible connectivity structure on local and global dynamics in large scale brain models.

    abstract::Functionally relevant large scale brain dynamics operates within the framework imposed by anatomical connectivity and time delays due to finite transmission speeds. To gain insight on the reliability and comparability of large scale brain network simulations, we investigate the effects of variations in the anatomical ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2009.07.007

    authors: Knock SA,McIntosh AR,Sporns O,Kötter R,Hagmann P,Jirsa VK

    更新日期:2009-09-30 00:00:00

  • Persistent neuronal labeling by retrograde fluorescent tracers: a comparison between Fast Blue, Fluoro-Gold and various dextran conjugates.

    abstract::The permanence of retrograde neuronal labeling by the fluorescent tracers Fast Blue, Fluoro-Gold, Mini-Ruby, Fluoro-Ruby and Fluoro-Emerald was investigated in adult rat spinal motorneurons at 1, 4, 12 and 24 weeks after tracer application to a transected muscle nerve. After 1 week, the largest number of retrogradely ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(97)02227-9

    authors: Novikova L,Novikov L,Kellerth JO

    更新日期:1997-06-06 00:00:00