Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

VISTO: An open-source device to measure exposure time in psychological experiments.

ABSTRACT: The study of higher cognitive processes often relies on the manipulation of bottom-up stimulus characteristics such as exposure time. While several software exist that can schedule the onset and offset time of a visual stimulus, the actual exposure time depends on several factors that are not easy to control, resulting in undesired variability within and across studies. Here we present VISTO, a simple device built on the Arduino platform that allows one to measure the exact onset and offset of a visual stimulus, and to test its synchronization with a trigger signal. The device is used to measure the profile of luminance waveforms in arbitrary analog/digital (AD) units, and the implications of these luminance profiles are discussed based on a model of information accumulation from visual exposure. Moreover, VISTO can be calibrated to match the brightness of each experimental monitor. VISTO allows for control of stimulus timing presentation, both in classical laboratory settings and in more complex settings as technology allows to use new display devices or acquisition equipment. In sum, VISTO allows one to:•measure the profile of luminance curves.•determine the exposure time of a visual stimulus.•measure the synchronization between a trigger signal and a visual stimulus.

SUBMITTER: De Cesarei A

PROVIDER: S-EPMC8374506 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Low-Cost Open-Source Device to Measure Maximal Inspiratory and Expiratory Pressures.

Project description:The measurement of maximal inspiratory (MIP) and maximal expiratory (MEP) pressures is a widely used technique to non-invasively evaluate respiratory muscle strength in clinical practice. The commercial devices that perform this test range from whole body plethysmographs to portable spirometers, both expensive and include a wide range of other respiratory tests. Given that a portable, low-cost, and specific option for MIP and MEP measuring device is not currently available in the market. A high-performance and easy-to-build prototype has been developed and the detailed technical information to easily reproduce it is freely released. A novel device is based on an Arduino microcontroller with a digital display, an integrated pressure transducer, and three-dimensional (3D) printed enclosure (total retail cost €80). The validation of the device was performed by comparison with a laboratory reference setting, and results showed accuracy within ±1%. As the device design is available according to the open-source hardware approach, measuring MIP/MEP can greatly facilitate easily available point-of-care devices for the monitoring of patients and, most important, for making this lung function measurement tool affordable to users in low- and middle-income countries.

| S-EPMC8427661 | biostudies-literature

OpenVape: An Open-Source E-Cigarette Vapor Exposure Device for Rodents.

Project description:The prevalence of "vaping" has recently seen significant increases in North America, especially in adolescents. However, the behavioral correlates of vaping are largely unexplored. The uptake of existing technologies meant for rodent vapor inhalation remains limited because of a lack of affordability and versatility (ability to be used with a variety of vaporizers). The OpenVape (OV) offers an open-source, low-cost solution that can be used in a variety of research contexts. Here, we present a specific use case, combining the OV apparatus with JUUL e-cigarettes. This apparatus consists of Arduino-operated vacuum pumps that deliver vapor directly from e-cigarettes to exposure chambers. The OV is easy to build and customize for any type of vaporizer (e.g., nicotine pod or tank; cannabis flower or concentrates). To test the OV, we performed biochemical verification and behavioral studies. The behavioral test (conditioned place preference, CPP) was conducted using adolescent and adult animals to assess developmental differences in the rewarding effects of nicotine vapor, as previously observed with injected nicotine. These findings demonstrate that even after brief exposures to nicotine vapor, pharmacologically relevant nicotine and cotinine levels could be detected in plasma, and significant CPP was observed, especially in adolescent rats which showed preference at shorter puff delivery durations (lower nicotine doses) compared with adults. Together, these findings suggest that OV provides an affordable, open-source option for preclinical behavioral research into the effects of vaping.

| S-EPMC7598908 | biostudies-literature

C-SPAM: an open-source time-resolved specimen vitrification device with light-activated molecules.

Project description:Molecular structures can be determined in vitro and in situ with cryo-electron microscopy (cryo-EM). Specimen preparation is a major obstacle in cryo-EM. Typical sample preparation is orders of magnitude slower than biological processes. Time-resolved cryo-EM (TR-cryo-EM) can capture short-lived states. Here, Cryo-EM sample preparation with light-activated molecules (C-SPAM) is presented, an open-source, photochemistry-coupled device for TR-cryo-EM that enables millisecond resolution and tunable timescales across broad biological applications.

| S-EPMC10833387 | biostudies-literature

A Wearable Open-Source electrical impedance tomography device.

Project description:Electrical impedance tomography (EIT) is medical imaging technique in which small electrical signals are used to map the electrical impedance distribution within the body. It is safe and non-invasive, which make it attractive for use in continuous monitoring or outpatient applications, but the high cost of commercial devices is an impediment to its adoption. Over the last 10 years, many research groups have developed their own EIT devices, but few designs for open-source EIT hardware are available. In this work, we present a complete open-source EIT system that is designed to be suitable for monitoring the lungs of free breathing subjects. The device is low-cost, wearable, and is designed to comply with the industry accepted safety standard for EIT. The device has been tested in two regimes: Firstly in terms of measurement uncertainty as a voltage measurement system, and secondly against a set of measures that have been proposed specifically for EIT hardware. The voltage measurement uncertainty of the device was measured to be - 0.7 % ± 0.36 mV. The EIT specific performance was measured in a phantom test designed to be as physiologically representative as practicable, and the device performed similarly to other published devices. This work will contribute to increased accessibility of EIT for study and will contribute to consensus on testing methodology for EIT devices.

| S-EPMC10973678 | biostudies-literature

A Low-Cost Open Source Device for Cell Microencapsulation.

Project description:Microencapsulation is a widely studied cell therapy and tissue bioengineering technique, since it is capable of creating an immune-privileged site, protecting encapsulated cells from the host immune system. Several polymers have been tested, but sodium alginate is in widespread use for cell encapsulation applications, due to its low toxicity and easy manipulation. Different cell encapsulation methods have been described in the literature using pressure differences or electrostatic changes with high cost commercial devices (about 30,000 US dollars). Herein, a low-cost device (about 100 US dollars) that can be created by commercial syringes or 3D printer devices has been developed. The capsules, whose diameter is around 500 µm and can decrease or increase according to the pressure applied to the system, is able to maintain cells viable and functional. The hydrogel porosity of the capsule indicates that the immune system is not capable of destroying host cells, demonstrating that new studies can be developed for cell therapy at low cost with microencapsulation production. This device may aid pre-clinical and clinical projects in low- and middle-income countries and is lined up with open source equipment devices.

| S-EPMC7696579 | biostudies-literature

An open source device for operant licking in rats.

Project description:We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior.

| S-EPMC5312574 | biostudies-literature

Feeding Experimentation Device (FED): A flexible open-source device for measuring feeding behavior.

Project description:BACKGROUND:Measuring food intake in rodents is a conceptually simple yet labor-intensive and temporally-imprecise task. Most commonly, food is weighed manually, with an interval of hours or days between measurements. Commercial feeding monitors are excellent, but are costly and require specialized caging and equipment. NEW METHOD:We have developed the Feeding Experimentation Device (FED): a low-cost, open-source, home cage-compatible feeding system. FED utilizes an Arduino microcontroller and open-source software and hardware. FED dispenses a single food pellet into a food well where it is monitored by an infrared beam. When the mouse removes the pellet, FED logs the timestamp to a secure digital (SD) card and dispenses a new pellet into the well. Post-hoc analyses of pellet retrieval timestamps reveal high-resolution details about feeding behavior. RESULTS:FED is capable of accurately measuring food intake, identifying discrete trends during light and dark-cycle feeding. Additionally, we show the utility of FED for measuring increases in feeding resulting from optogenetic stimulation of agouti-related peptide neurons in the arcuate nucleus of the hypothalamus. COMPARISON TO EXISTING METHODS:With a cost of ?$350 per device, FED is >10× cheaper than commercially available feeding systems. FED is also self-contained, battery powered, and designed to be placed in standard colony rack cages, allowing for monitoring of true home cage feeding behavior. Moreover, FED is highly adaptable and can be synchronized with emerging techniques in neuroscience, such as optogenetics, as we demonstrate here. CONCLUSIONS:FED allows for accurate, precise monitoring of feeding behavior in a home cage setting.

| S-EPMC4884551 | biostudies-literature

An Open-Source Framework for Automated High-Throughput Cell Biology Experiments.

Project description:Modern data analysis methods, such as optimization algorithms or deep learning have been successfully applied to a number of biotechnological and medical questions. For these methods to be efficient, a large number of high-quality and reproducible experiments needs to be conducted, requiring a high degree of automation. Here, we present an open-source hardware and low-cost framework that allows for automatic high-throughput generation of large amounts of cell biology data. Our design consists of an epifluorescent microscope with automated XY stage for moving a multiwell plate containing cells and a perfusion manifold allowing programmed application of up to eight different solutions. Our system is very flexible and can be adapted easily for individual experimental needs. To demonstrate the utility of the system, we have used it to perform high-throughput Ca2+ imaging and large-scale fluorescent labeling experiments.

| S-EPMC8498207 | biostudies-literature

Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments.

Project description:Laboratory behavioural tasks are an essential research tool. As questions asked of behaviour and brain activity become more sophisticated, the ability to specify and run richly structured tasks becomes more important. An increasing focus on reproducibility also necessitates accurate communication of task logic to other researchers. To these ends, we developed pyControl, a system of open-source hardware and software for controlling behavioural experiments comprising a simple yet flexible Python-based syntax for specifying tasks as extended state machines, hardware modules for building behavioural setups, and a graphical user interface designed for efficiently running high-throughput experiments on many setups in parallel, all with extensive online documentation. These tools make it quicker, easier, and cheaper to implement rich behavioural tasks at scale. As important, pyControl facilitates communication and reproducibility of behavioural experiments through a highly readable task definition syntax and self-documenting features. Here, we outline the system's design and rationale, present validation experiments characterising system performance, and demonstrate example applications in freely moving and head-fixed mouse behaviour.

| S-EPMC8769647 | biostudies-literature

OPETH: Open Source Solution for Real-Time Peri-Event Time Histogram Based on Open Ephys.

Project description:Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Decisions made by the experimenter during electrophysiology recording largely determine recording quality, duration of the project and value of the collected data. Therefore, online feedback aiding these decisions can lower monetary and time investment, and substantially speed up projects as well as allow novel studies otherwise not possible due to prohibitively low throughput. Real-time feedback is especially important in studies that involve optogenetic cell type identification by enabling a systematic search for neurons of interest. However, such tools are scarce and limited to costly commercial systems with high degree of specialization, which hitherto prevented wide-ranging benefits for the community. To address this, we present an open-source tool that enables online feedback during electrophysiology experiments and provides a Python interface for the widely used Open Ephys open source data acquisition system. Specifically, our software allows flexible online visualization of spike alignment to external events, called the online peri-event time histogram (OPETH). These external events, conveyed by digital logic signals, may indicate photostimulation time stamps for in vivo optogenetic cell type identification or the times of behaviorally relevant events during in vivo behavioral neurophysiology experiments. Therefore, OPETH allows real-time identification of genetically defined neuron types or behaviorally responsive populations. By allowing "hunting" for neurons of interest, OPETH significantly reduces experiment time and thus increases the efficiency of experiments that combine in vivo electrophysiology with behavior or optogenetic tagging of neurons.

| S-EPMC7251067 | 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