Setups

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Setup name	Location	Setup types	Specifications	Equipment #
Zero Maze #1 Duplicate Delete	-	Elevated zero maze	-	1
Figure 8 Maze #9 Duplicate Delete	-	Figure eight maze	-	1
Cheddar Maze Duplicate Delete	-	Cheeseboard maze	-	1
Parmesan Maze Duplicate Delete	-	Cheeseboard maze	-	1
Gruyere Maze Duplicate Delete	-	Cheeseboard maze	-	1
Lore testing PE Duplicate Delete	-	Barnes maze	-	-
pe-test-ivan Duplicate Delete	-	Barnes maze	-	-
Maze #1 Duplicate Delete	-	Cheeseboard maze	-	-

8 Setups

Setups

A setup describes a specific physical rig, maze, or apparatus in your lab where experiments are conducted. Setups are where procedures, data acquisition, behaviors, and manipulations take place. Each setup belongs to a setup type and can have equipment and specifications associated with it.

How It Fits Together

Setups are part of a two-level hierarchy for describing experimental apparatus:

Setup Type Category — The broad experimental condition (e.g., "Freely Moving Awake", "Head-Fixed Awake", "In Vitro"). This is a field on the setup type.
Setup Type — A shared, standardized type of apparatus (e.g., "Open Field Arena", "Linear Track", "Two-Photon Microscope"). Defined in taxonomies and available to everyone.
Setup (this page) — Your lab's specific physical rig (e.g., "EPM Rig B, Room 108" or "Two-Photon Rig 1, Room 312"). Belongs to your groups.

In a behavioral experiment, a behavior record links a behavioral assay (how you run a paradigm) with a setup (where you run it) and the subjects involved.

Example

Level	Example
Setup Type Category	Freely Moving Awake
Setup Type	Open Field Arena
Setup	"Open Field, Room 204" — 50×50 cm arena, Room 204

Fields

Name: The name of the setup (required).
Setup type: The standardized apparatus type (e.g., "Open Field Arena", "Linear Track"). Each setup type has a category describing the experimental condition (Freely Moving Awake, Head-Fixed Awake, etc.) (required).
Location: Physical location, e.g., "Room 302B, Neuroscience Building".
Description: A description of the setup.
Image: An image of the setup.
Specifications: Name-value pairs describing dimensions, weight, or other physical properties.
Authenticated groups: Only shown during creation. Assign one or more groups. Permissions can be adjusted later on the "Manage permissions" page (required).
Public access: Determines if the setup is publicly available or accessible only through the private portal.

Equipment

A setup is composed of equipment — the individual hardware devices that make up the rig. Equipment entries are added to a setup to document which devices are installed and how they are configured. Each equipment entry can optionally link to a shared hardware device from the resources library (e.g., a specific amplifier model from a supplier), and may include coordinates describing its physical placement.

Equipment types include:

Data Acquisition — Amplifiers, cameras, EEG/EMG systems, fiber photometry, miniscopes, MRI, motion tracking, etc.
Behavioral & Stimulation — Behavior rigs, speakers, lasers, LED drivers, treadmills, running wheels, stimulation devices
Environmental Controllers — Anti-vibration tables, noise isolation chambers, thermal and humidity controllers
Surgical Equipment — Stereotaxic frames, micromanipulators, microscopes, anesthesia and injection systems
Miscellaneous — Computers, monitors, microcontrollers, single-board computers, electronic components

See the Equipment tab above for a full list of equipment types and their fields.

Permissions

Setups define the overall permissions level for equipment. You manage permissions through the management tab, where you can assign individual users and groups access levels to a setup. Setups have four permission levels: membership (read access), change permissions, managers, and owners. For more information on permissions, please see the documentation.

API Access

The API allows for programmable access to setups, enabling you to read, edit, and delete setups through the API. For details about the setup's fields and data structure, refer to the documentation.

Equipment

Equipment forms the backbone of setups, comprising various hardware devices and consumable stocks designed to acquire, monitor, record, stimulate, or manipulate environmental variables and subject responses. These equipment are critical for creating controlled experimental conditions, collecting data, and delivering stimuli in neuroscience research. Each equipment type has specific applications and functions within setups. Equipment types share relationships, but fields are tailored to the various equipment-types.

Types of Equipment:

Data Acquisition

Amplifier: Amplifies electrical signals from biological sources such as neurons or muscles, making them suitable for processing and analysis. Essential for electrophysiological studies to ensure signal clarity.
Camera: Captures video or still images to monitor subject behavior, movement, or environmental changes, supporting behavioral analysis and motion tracking.
Data Acquisition System: Integrates hardware and software to collect, process, and store data from multiple sources in real-time.
Electroencephalography System (EEG): Records electrical activity from the scalp to study brain function and neural dynamics in humans or animals.
Electromyography Machine (EMG): Measures muscle electrical activity, aiding in studies of motor control and neuromuscular disorders.
Ephys Rig: A comprehensive setup for electrophysiological recordings, including extracellular and intracellular methods for studying neural activity.
Fiber Photometry System: Monitors neural activity by measuring calcium or neurotransmitter dynamics in vivo using fluorescence-based techniques.
Force Plate: Measures forces exerted by subjects, commonly used in motor control, biomechanics, and locomotion studies.
Humidity Sensor: Monitors humidity levels in experimental setups to ensure stable environmental conditions.
Light Sensor: Detects and measures light intensity, often used in studies involving photosensitivity or optogenetics.
Magnetic Resonance Imaging System (MRI): Produces detailed anatomical and functional images of the brain using magnetic fields.
Magnetoencephalography System (MEG): Detects magnetic fields produced by neural activity, providing high temporal resolution for brain studies.
Magnetometer: Measures magnetic fields, often used in studies involving brain stimulation or motion tracking.
Microphone: Records audio data, including vocalizations or environmental sounds, supporting auditory and behavioral studies.
Miniscope: Miniature fluorescence microscopes designed for imaging neural activity in freely moving animals.
Motion Tracking System: Tracks subject movement in real-time for behavioral or neural experiments.
Ophys Rig: Combines optical imaging with physiological recordings for simultaneous monitoring of neural activity.
Optical Coherence Tomography (OCT): Uses light waves to capture detailed cross-sectional images of tissues, such as brain slices.
Oscilloscope: Visualizes electrical signals in real-time, aiding in diagnostics and monitoring.
Photodetector: Measures light intensity in fluorescence or optical experiments.
Signal Processing Unit: Processes and filters raw data from recording devices for analysis.
Single Photon Emission Computed Tomography (SPECT): Functional imaging method using gamma rays for studying metabolic activity.
Temperature Sensor: Monitors thermal conditions in experimental setups to ensure stability and accuracy.
Ultrasound Imaging System: Captures high-resolution internal images using sound waves, useful for structural studies.

Behavioral and Stimulation Tools

Behavior Rig: Designed for studying animal behavior under controlled conditions, often equipped with cameras, sensors, and stimulus delivery systems.
Iontophoresis Stimulator: Applies electrical currents to deliver charged molecules to tissues with high precision.
Laser: Provides focused light for stimulation, imaging, or tissue ablation in experimental setups.
LED Driver: Controls light-emitting diodes (LEDs) for visual experiments or optogenetics, enabling precise light modulation.
Light Emitter: Provides controlled light stimuli, often used in optogenetics or photosensitivity studies.
Running Wheel: Tracks locomotor activity or provides exercise for experimental subjects.
Speaker: Delivers auditory stimuli, such as tones or sounds, for auditory research or conditioning experiments.
Stimulation Device: Delivers controlled electrical, magnetic, or mechanical stimulation to tissues.
Treadmill: Used for locomotion studies, often combined with virtual reality setups for precise tracking.

Environmental Controllers

Anti-Vibration Table: Provides a stable, vibration-free platform for precision experiments, such as microscopy or electrophysiology setups.
Floating Air Platform: Minimizes external vibrations for highly sensitive experiments, ensuring precise and reliable measurements.
Humidity Controller: Monitors and adjusts humidity levels in experimental setups, critical for environmental studies and tissue preservation.
Noise Isolation Chamber: Minimizes external noise, ensuring controlled experimental conditions for sensitive studies.
Thermal Controller: Regulates temperature in experimental environments or for subject maintenance, ensuring optimal conditions.

Surgical Equipment

Anesthesia System: Ensures safe and controlled administration of anesthesia to experimental subjects during procedures.
Injection System: Delivers precise volumes of substances into biological tissues or cells.
Micromanipulator: Precisely positions electrodes or devices during surgeries or neural recordings, ensuring accurate placement.
Microscope: Provides high-resolution imaging of biological samples, with specialized models for fluorescence, confocal, or two-photon imaging.
Stereotaxic Frame: Stabilizes subjects during surgeries or recordings, enabling precise targeting of brain regions.
Surgical Power Tool: Includes drills or other tools used for cranial surgeries or electrode implantations.
Perfusion System: Maintains tissue viability by providing oxygenated solutions during experiments.

Miscellaneous

Biosafety Cabinet: Creates a sterile environment for handling biological materials, ensuring the safety of users and samples.
Computer: Runs software for data collection, analysis, and control of experimental equipment. Includes desktop workstations or high-performance servers configured for specialized tasks.
Electronic Component: Fundamental building blocks of electronic systems, including resistors, capacitors, transistors, and modules. Used for custom hardware solutions in signal processing, device control, or stimulation systems.
Fume Hood: Provides a controlled environment to handle volatile chemicals safely, protecting users from hazardous fumes.
Glass Micropipette Puller: Creates fine-tipped glass micropipettes for use in microinjections or electrophysiological recordings.
Microcontroller: Compact devices designed to control specific operations, such as managing stimuli delivery or data acquisition. Popular examples include Arduino, used for rapid prototyping and custom experiment control systems.
Monitor: Displays visual stimuli for subjects or experimental data for researchers.
Single-Board Computer: Lightweight, versatile computers like Raspberry Pi that run custom software for experimental control, automation, and localized data processing.

Fields

Name: The name of the equipment (required).
Type: The type of equipment (required).
Setup: The setup the equipment is a part of (required).
Notes: Notes to the equipment.
Date and Time: Date and time the equipment is installed in the setup.
Consumable: Consumable used in the equipment.
Hardware Device: Hardware device used to perform the equipment.
Type Details: Each type has a number of type-specific fields. Learn more on the documentation website.
Coordinate System: The coordinate system.
Coordinates: Where the equipment is located. Learn more about the types of coordinate systems and specific values on the documentation website.

Permissions

equipment inherits permissions from projects via the subject associate with the entry. For more information on permissions, please see the documentation.

Equipment API Access

The API allows for programmable access to Equipment, enabling you to read, edit, and delete Equipment through the API. For details about the Equipment's fields and data structure, refer to the documentation.