Equipment model
Table of contents
Introduction
Equipment refer to the setup and utilization of various devices and sensors designed to monitor, record, or manipulate environmental variables or subject responses. These equipment are critical for creating controlled experimental conditions, collecting data, and delivering stimuli. Each equipment type has specific applications and functions within setups. While equipment types share relationships, fields are tailored to the various equipment types. The types of equipment currently supported by BrainSTEM are listed below.
Fields
| Field | Description |
|---|---|
Equipment name | Name of the equipment (required). Example: “Ephys amplifier” or “Ceiling mounted camera” |
Type of equipment | Type of equipment (required). Selected from predefined types. Example: “Camera”, “Microphone”. See options below |
Setup | The setup the equipment is installed in (required). Must reference an existing setups. Example: “Behavior room A setup” |
Date and time of the installation of the equipment | Date and time the equipment was installed. Example: “2024-03-22 09:00:00” |
Supplier | Supplier filter for consumables (optional). Used to filter available consumables by supplier. |
Consumable | Consumable used as part of the equipment installation (optional). Example: “HD webcam model XYZ” |
Hardware device supplier | Supplier filter for hardware devices (optional). Used to filter available hardware devices by supplier. |
Hardware device | Hardware device used as part of the equipment (optional). Example: “Recording computer #2” |
Notes | Notes about the equipment (string). Example: “Camera positioned at 45-degree angle” |
Coordinates | Coordinate system for equipment positioning (required). Selected from predefined systems. Example: “External XYZ Coordinates with Angles”. See options below |
Types of equipment
These are the available type options for equipment:
See the schema for field details: Equipment types.
Data acquisition
Amplifier: Amplifies bioelectrical signals (neural or muscular) for recording and analysis in electrophysiology.
Camera: Captures video or still images to monitor behavior, movement, and experimental context.
Data acquisition system: Acquires, synchronizes, and stores signals from multiple sources in real time.
Electroencephalography system (EEG): Records scalp electrical activity to study large‑scale brain dynamics and function.
Electromyography machine: Measures muscle electrical activity for motor control and neuromuscular studies.
Ephys rig: Integrated setup for extra‑/intracellular electrophysiological recordings of neural activity.
Fiber photometry system: Measures population fluorescence (e.g., calcium or neuromodulators) in vivo via fiber‑coupled optics.
Force plate: Measures ground reaction forces for locomotion, biomechanics, and motor control.
Humidity sensor: Monitors ambient humidity in experimental environments.
Light sensor: Measures light intensity for stimulus calibration and environmental monitoring.
Magnetic resonance imaging (MRI) system: Generates anatomical or functional images using magnetic fields and radiofrequency pulses.
Magnetoencephalography (MEG) system: Detects magnetic fields generated by neural activity with high temporal resolution.
Magnetometer: Measures magnetic fields for stimulation alignment, motion tracking, or environmental monitoring.
Microphone: Records audio (vocalizations, stimuli, ambient) for auditory and behavioral studies.
Miniscope: Head‑mounted fluorescence microscope for imaging neural activity in freely moving animals.
Motion tracking system: Tracks 2D/3D movement and pose in real time.
Ophys rig: Optical physiology setup combining imaging with physiological readouts.
Optical Coherence Tomography (OCT): Micrometer‑scale, cross‑sectional imaging of tissue using low‑coherence interferometry.
Oscilloscope: Displays and analyzes electrical waveforms in real time for diagnostics and monitoring.
Photodetector: Detects and quantifies light intensity in optical experiments.
Signal processing unit: Conditions, filters, and digitizes signals prior to analysis.
Single-photon emission computed tomography (SPECT): Gamma‑ray functional imaging for metabolic and physiological activity.
Temperature sensor: Monitors temperature of environments, apparatus, or subjects.
Ultrasound imaging system: Produces internal images using high‑frequency sound for structural and functional studies.
Behavioral and stimulation tools
Behavior rig: Controlled environment with sensors and actuators for behavioral experiments.
Iontophoresis stimulator: Delivers charged molecules into tissue via controlled electrical current.
Laser: Provides focused light for stimulation, ablation, or imaging.
LED Driver: Controls LEDs for visual stimuli or optogenetic protocols with precise intensity and timing.
Light emitter: Delivers controlled light stimuli to subjects or preparations.
Running Wheel: Measures locomotion and provides voluntary exercise.
Speaker: Delivers auditory stimuli (tones, noise, vocalizations) for research and conditioning.
Stimulation device: Applies controlled electrical, magnetic, or mechanical stimulation to tissue.
Treadmill: Enables controlled locomotion, often combined with VR or tracking systems.
Environmental controllers
Anti-vibration table: Isolates setups from external vibrations for precision experiments.
Floating air platform: Actively isolates against vibrations for highly sensitive measurements.
Humidity controller: Regulates humidity to maintain stable environmental conditions.
Noise isolation chamber: Reduces acoustic noise to protect sensitive recordings and experiments.
Thermal controller: Regulates temperature of environments, equipment, or subjects.
Surgical equipment
Anesthesia system: Delivers and monitors anesthesia safely during procedures.
Injection system: Dispenses precise volumes into tissues or cells.
Micromanipulator: Precisely positions tools or electrodes during surgery and recordings.
Stereotaxic frame: Immobilizes subjects and enables atlas‑based, precise targeting of brain regions.
Surgical power tool: Powered instruments (e.g., drills) for cranial procedures and implantations.
Perfusion system: Provides oxygenated or conditioned solutions to maintain tissue viability.
Miscellaneous
Biosafety cabinet: Provides a sterile, contained workspace for handling biological materials.
Computer: Runs acquisition, control, and analysis software within the setup.
Electronic component: Discrete parts or modules (e.g., resistors, sensors, drivers) for custom hardware and integration.
Fume hood: Vented enclosure for safe handling of volatile chemicals.
Glass micropipette puller: Fabricates fine‑tipped glass micropipettes for injections or recordings.
Microcontroller (e.g. Arduino): Embedded controller for stimulus delivery, device control, or data acquisition (e.g., Arduino).
Microscope: Optical instrument for high‑resolution imaging (e.g., brightfield, fluorescence, confocal, two‑photon).
Monitor: Displays visual stimuli to subjects or experimental data to researchers.
Single-board computer (e.g. Raspberry Pi): Compact computer for control, automation, and edge processing (e.g., Raspberry Pi).
Coordinate system options
Available coordinate system options for equipment:
| Type | Description |
|---|---|
| External XYZ Coordinates with Angles | Absolute external coordinates. This can be used to describe, e.g., a camera’s position in a room |
| Stereotaxic Bregma-Based Absolute Coordinates | Stereotaxic coordinates referenced to the bregma point with absolute positioning |
| Stereotaxic Bregma-Based Surface Coordinates with Depth | Stereotaxic coordinates referenced to bregma with surface positioning and depth measurement |
| Stereotaxic Lambda-Based Absolute Coordinates | Stereotaxic coordinates referenced to the lambda point with absolute positioning |
| Stereotaxic Lambda-Based Surface Coordinates with Depth | Stereotaxic coordinates referenced to lambda with surface positioning and depth measurement |
| Common Coordinate Framework XYZ Absolute Coordinates | Coordinates based on the Common Coordinate Framework for standardized brain mapping |
A detailed list of the fields in Coordinate system can be found on the Coordinate systems page.
Permissions
Equipment inherit permissions through the setup associated with them.
Visit the permissions page to learn more.
API access
The API allows for programmable access to equipment. Learn more about the equipment fields and data structure on the Equipment API page.