Setup types are broad sets of agreed upon classifications of setups and also serves as a foundation for behavioral paradigms. In BrainSTEM, setup types are a shared model across users. Behavioral paradigm are linked to a specific setup type, so that that paradigm is defined within that type of setup.
Categories of setups:
- In Vitro:
Focuses on isolated cells or tissues maintained outside of a living organism. It offers maximal experimental control and mechanistic clarity but lacks natural systemic context.
- Ex Vivo:
Involves intact or semi-intact tissue preparations retaining some network-level organization. Balances controllability with partial network complexity, bridging the gap between single cells and whole organisms.
- Anesthetized In Vivo:
A living subject under anesthesia, allowing for controlled interventions and stable physiological conditions. Ideal for surgical procedures (e.g., implanting electrodes, optical fibers) and stable, artifact-free recordings.
- Head-Fixed Awake:
The subject is awake but head-restrained, enabling stable recordings and controlled stimuli while preserving aspects of natural sensory and cognitive processing.
- Voluntarily Stationary Awake:
The subject is awake and alert but chooses to remain still without physical restraint. Typically employed with non-invasive measurement techniques such as external imaging or surface-level recordings. It enables the investigation of cognitive, sensory, and behavioral processes under more naturalistic conditions than head fixation while avoiding the invasiveness of surgical interventions.
- Freely Moving Awake:
It allows the subject to engage in a full range of natural behaviors, often after implantations, which are performed in a separate anesthetized session. This captures the complexity of behavioral and ecological validity at the cost of reduced environmental control.
Submission process
Anyone can submit setup types or submit changes to existing ones, but all submissions must be approved before they are available for usage. Please see existing entries for examples as to what to submit.
Fields
- Name: The name of the setup type (required; must be unique).
- Category: Category of the setup (required).
- Description: A general description of the setup type.
Permissions
Once a entry has been approved it becomes available to everyone.
API Access
The API allows for programmable access, enabling you to read, edit, and delete entries through the API. For details about the fields and data structure, refer to the Setup type API endpoint documentation.
