Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protocol for precise signal synchronization of electrophysiology, videography, and audio recordings using a custom-made pulse generator.

ABSTRACT: Precise signal synchronization is vital for accurate analysis in systems neuroscience. Here, we present a protocol for synchronizing electrophysiology, videography, and audio recordings using a custom-made pulse generator. We describe steps for building the pulse generator, installing software, connecting devices, and running experimental sessions. We then detail signal analysis, temporal alignment, and duration normalization. This protocol offers flexibility and cost-effectiveness, addressing limited shared knowledge and providing a solution for signal synchronization in various experimental setups.

SUBMITTER: Dagher S

PROVIDER: S-EPMC10199308 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Protocol for precise signal synchronization of electrophysiology, videography, and audio recordings using a custom-made pulse generator.

Dagher Sarah S Ishiyama Shimpei S

STAR protocols 20230512 2

Precise signal synchronization is vital for accurate analysis in systems neuroscience. Here, we present a protocol for synchronizing electrophysiology, videography, and audio recordings using a custom-made pulse generator. We describe steps for building the pulse generator, installing software, connecting devices, and running experimental sessions. We then detail signal analysis, temporal alignment, and duration normalization. This protocol offers flexibility and cost-effectiveness, addressing l ...[more]

PMID: 37178112

Similar Datasets

In vivo imaging of the GnRH pulse generator reveals a temporal order of neuronal activation and synchronization during each pulse.

Project description:A hypothalamic pulse generator located in the arcuate nucleus controls episodic release of gonadotropin-releasing hormone (GnRH) and luteinizing hormone (LH) and is essential for reproduction. Recent evidence suggests this generator is composed of arcuate "KNDy" cells, the abbreviation based on coexpression of kisspeptin, neurokinin B, and dynorphin. However, direct visual evidence of KNDy neuron activity at a single-cell level during a pulse is lacking. Here, we use in vivo calcium imaging in freely moving female mice to show that individual KNDy neurons are synchronously activated in an episodic manner, and these synchronized episodes always precede LH pulses. Furthermore, synchronization among KNDy cells occurs in a temporal order, with some subsets of KNDy cells serving as "leaders" and others as "followers" during each synchronized episode. These results reveal an unsuspected temporal organization of activation and synchronization within the GnRH pulse generator, suggesting that different subsets of KNDy neurons are activated at pulse onset than afterward during maintenance and eventual termination of each pulse. Further studies to distinguish KNDy "leader" from "follower" cells is likely to have important clinical significance, since regulation of pulsatile GnRH secretion is essential for normal reproduction and disrupted in pathological conditions such as polycystic ovary syndrome and hypothalamic amenorrhea.

| S-EPMC8833213 | biostudies-literature

Identifying the sources of the pulse artefact in EEG recordings made inside an MR scanner.

Project description:EEG recordings made during concurrent fMRI are confounded by the pulse artefact (PA), which although smaller than the gradient artefact is often more problematic because of its variability over multiple cardiac cycles. A better understanding of the PA is needed in order to generate improved methods for reducing its effect in EEG-fMRI experiments. Here we performed a study aimed at identifying the relative contributions of three putative sources of the PA (cardiac-pulse-driven head rotation, the Hall effect due to pulsatile blood flow and pulse-driven expansion of the scalp) to its amplitude and variability. EEG recordings were made from 6 subjects lying in a 3T scanner. Accelerometers were fixed on the forehead and temple to monitor head motion. A bite-bar and vacuum cushion were used to restrain the head, thus greatly attenuating the contribution of cardiac-driven head rotation to the PA, while an insulating layer placed between the head and the EEG electrodes was used to eliminate the Hall voltage contribution. Using the root mean square (RMS) amplitude of the PA averaged over leads and time as a measure of the PA amplitude, we found that head restraint and insulating layer reduced the PA by 61% and 42%, respectively, when compared with the PA induced with the subject relaxed, indicating that cardiac-pulse-driven head rotation is the dominant source of the PA. With both the insulating layer and head restraint in place, the PA was reduced in RMS amplitude by 78% compared with the relaxed condition, the remaining PA contribution resulting from scalp expansion or residual head motion. The variance of the PA across cardiac cycles was more strongly reduced by the insulating layer than the head restraint, indicating that the flow-induced Hall voltage makes a larger contribution than pulse-driven head rotation to the variability of the PA.

| S-EPMC3601330 | biostudies-literature

PSG-Audio, a scored polysomnography dataset with simultaneous audio recordings for sleep apnea studies.

Project description:The sleep apnea syndrome is a chronic condition that affects the quality of life and increases the risk of severe health conditions such as cardiovascular diseases. However, the prevalence of the syndrome in the general population is considered to be heavily underestimated due to the restricted number of people seeking diagnosis, with the leading cause for this being the inconvenience of the current reference standard for apnea diagnosis: Polysomnography. To enhance patients' awareness of the syndrome, a great endeavour is conducted in the literature. Various home-based apnea detection systems are being developed, profiting from information in a restricted set of polysomnography signals. In particular, breathing sound has been proven highly effective in detecting apneic events during sleep. The development of accurate systems requires multitudinous datasets of audio recordings and polysomnograms. In this work, we provide the first open access dataset, comprising 212 polysomnograms along with synchronized high-quality tracheal and ambient microphone recordings. We envision this dataset to be widely used for the development of home-based apnea detection techniques and frameworks.

| S-EPMC8333307 | biostudies-literature

Custom-made health-care: an experimental investigation.

Project description:BackgroundPhysicians' financial interests might conflict with the best service to patients. It is essential to gain a thorough understanding of the effect of remuneration systems on physician behaviour.MethodsWe conducted a controlled laboratory experiment using a within-subject design to investigate physician behaviour underpayment heterogeneity. Each physician provided medical care to patients whose treatments were paid for under fee-for-service (FFS) or capitation (CAP).ResultsWe observed that physicians customized their care in response to the payment system. FFS patients received considerably more medical care than did CAP patients with the same illness and treatment preference. Physicians over-served FFS patients and under-served CAP patients. After a CAP payment reduction, we observed neither a quantity reduction under CAP nor a spillover in FFS patients' treatment.ConclusionsThe results suggest that, in our experimental model, fee regulation can be used to some extent to control physician spending since we did not identify a behavioural response to the CAP payment cut. Physicians did not recoup lost income by altering treatment behaviour toward CAP and/or FFS patients. Experimental economics is an excellent tool for ensuring the welfare of all those involved in the health system. Further research should investigate payment incentives as a means of developing health care teams that are more efficient.

| S-EPMC7749502 | biostudies-literature

HomeBank: An Online Repository of Daylong Child-Centered Audio Recordings.

Project description:HomeBank is introduced here. It is a public, permanent, extensible, online database of daylong audio recorded in naturalistic environments. HomeBank serves two primary purposes. First, it is a repository for raw audio and associated files: one database requires special permissions, and another redacted database allows unrestricted public access. Associated files include metadata such as participant demographics and clinical diagnostics, automated annotations, and human-generated transcriptions and annotations. Many recordings use the child-perspective LENA recorders (LENA Research Foundation, Boulder, Colorado, United States), but various recordings and metadata can be accommodated. The HomeBank database can have both vetted and unvetted recordings, with different levels of accessibility. Additionally, HomeBank is an open repository for processing and analysis tools for HomeBank or similar data sets. HomeBank is flexible for users and contributors, making primary data available to researchers, especially those in child development, linguistics, and audio engineering. HomeBank facilitates researchers' access to large-scale data and tools, linking the acoustic, auditory, and linguistic characteristics of children's environments with a variety of variables including socioeconomic status, family characteristics, language trajectories, and disorders. Automated processing applied to daylong home audio recordings is now becoming widely used in early intervention initiatives, helping parents to provide richer speech input to at-risk children.

| S-EPMC5570530 | biostudies-other

Bio-inspired benchmark generator for extracellular multi-unit recordings.

Project description:The analysis of multi-unit extracellular recordings of brain activity has led to the development of numerous tools, ranging from signal processing algorithms to electronic devices and applications. Currently, the evaluation and optimisation of these tools are hampered by the lack of ground-truth databases of neural signals. These databases must be parameterisable, easy to generate and bio-inspired, i.e. containing features encountered in real electrophysiological recording sessions. Towards that end, this article introduces an original computational approach to create fully annotated and parameterised benchmark datasets, generated from the summation of three components: neural signals from compartmental models and recorded extracellular spikes, non-stationary slow oscillations, and a variety of different types of artefacts. We present three application examples. (1) We reproduced in-vivo extracellular hippocampal multi-unit recordings from either tetrode or polytrode designs. (2) We simulated recordings in two different experimental conditions: anaesthetised and awake subjects. (3) Last, we also conducted a series of simulations to study the impact of different level of artefacts on extracellular recordings and their influence in the frequency domain. Beyond the results presented here, such a benchmark dataset generator has many applications such as calibration, evaluation and development of both hardware and software architectures.

| S-EPMC5324125 | biostudies-literature

Audio recordings dataset of grazing jaw movements in dairy cattle.

Project description:This dataset is composed of correlated audio recordings and labels of ingestive jaw movements performed during grazing by dairy cattle. Using a wireless microphone, we recorded sounds of three Holstein dairy cows grazing short and tall alfalfa and short and tall fescue. Two experts in grazing behavior identified and labeled the start, end, and type of each jaw movement: bite, chew, and chew-bite (compound movement). For each segment of raw audio corresponding to a jaw movement we computed four well-known features: amplitude, duration, zero crossings, and envelope symmetry. These features are in the dataset and can be used as inputs to build automated methods for classification of ingestive jaw movements. Cow's grazing behavior can be monitored and characterized by identifying and analyzing these masticatory events.

| S-EPMC7214825 | biostudies-literature

Rhythmic synchronization tapping to an audio-visual metronome in budgerigars.

Project description:In all ages and countries, music and dance have constituted a central part in human culture and communication. Recently, vocal-learning animals such as parrots and elephants have been found to share rhythmic ability with humans. Thus, we investigated the rhythmic synchronization of budgerigars, a vocal-mimicking parrot species, under controlled conditions and a systematically designed experimental paradigm as a first step in understanding the evolution of musical entrainment. We trained eight budgerigars to perform isochronous tapping tasks in which they pecked a key to the rhythm of audio-visual metronome-like stimuli. The budgerigars showed evidence of entrainment to external stimuli over a wide range of tempos. They seemed to be inherently inclined to tap at fast tempos, which have a similar time scale to the rhythm of budgerigars' natural vocalizations. We suggest that vocal learning might have contributed to their performance, which resembled that of humans.

| S-EPMC3216601 | biostudies-literature

Establishment of an open data policy for Journal of Educational Evaluation for Health Professions, appreciation for invited reviewers, and acknowledgement of volunteers who made audio recordings.

Project description: Not available

| S-EPMC5801429 | biostudies-literature

Studying naturalistic human communication using dual-EEG and audio-visual recordings.

Project description:We present a protocol to study naturalistic human communication using dual-electroencephalography (EEG) and audio-visual recordings. We describe preparatory steps for data collection including setup preparation, experiment design, and piloting. We then describe the data collection process in detail which consists of participant recruitment, experiment room preparation, and data collection. We also outline the kinds of research questions that can be addressed with the current protocol, including several analysis possibilities, from conversational to advanced time-frequency analyses. For complete details on the use and execution of this protocol, please refer to Drijvers and Holler (2022).1.

| S-EPMC10511849 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data