Procedure model
Table of contents
Introduction
Procedures cover surgical procedures and other methods that allow tracking or recording from subject(s). Procedures have type-specific fields tailored to various procedure types. The types of procedures currently supported by BrainSTEM are listed below. A procedure is described by the fields in the next section.
Fields
| Field | Description |
|---|---|
Type of procedure | Type of procedure (required). Selected from predefined types. Example: “Optic fiber implant”. See options below |
Subject | The subject the procedure was performed on (required). Must reference an existing subjects. Example: “Mouse_01” |
Date and time of the procedure | Date and time the procedure was performed. Example: “2024-03-22 10:30:00” |
Inventory | Inventory filter for consumable stocks (optional). Used to filter available consumable stocks by inventory. |
Consumable stock | Consumable stock used in the procedure (optional). Must reference an existing consumable stock. Example: “32-channel silicon probe” |
Setup | Setup filter for equipment (optional). Used to filter available equipment by setup. |
Equipment | Equipment used in the procedure (optional). Must reference existing equipment. Example: “Intan RHD2000” |
Atlas | Brain atlas filter for brain regions (optional). Used to filter available brain regions by atlas. |
Brain region | Target brain region of the procedure (optional). Must reference an existing brain region. Example: “Hippocampus CA1” |
Notes | Notes about the procedure (string). Example: “Implant placed successfully with minimal bleeding” |
Types of procedures
These are the available type options for procedures:
See the schema for field details: Procedure types.
Surgical Procedures
Anesthesia: Administration of anesthetic agents to provide analgesia and sedation during procedures.
Burr hole: Drilling small openings in the skull to access brain tissue or place probes/electrodes.
Cranial window: Replacing a skull section with a transparent window for optical access to the cortical surface.
Craniectomy: Permanent removal of a skull portion to provide extended access to brain tissue.
Craniotomy: Temporary removal of a skull flap to expose brain, with the bone replaced afterwards.
Headcap: Protective cap applied to the skull to cover and secure implants post‑surgery.
Head fixation: Stabilizing the head mechanically to ensure immobility during recordings or procedures.
Headpost: Implanting a post to secure the head during procedures or behavioral tasks.
Implant Procedures
Blood pressure sensor implant: Implanting a device to continuously monitor blood pressure within the cardiovascular system.
Breathing sensor implant: Implanting sensors to monitor respiratory rate, pattern, and function.
GRIN (Gradient Index) lens implant: Implanting a gradient‑index lens to enable deep‑brain optical imaging.
Catheter implant: Placing a catheter for drug delivery or physiological fluid access/monitoring.
ECG implant (Electrocardiography): Implanting electrodes to record the heart’s electrical activity.
EEG implant (Electroencephalography): Implanting electrodes to record electrical activity of the brain.
EMG implant (Electromyography): Implanting electrodes to record muscle electrical activity.
Nerve cuff implant: Placing a cuff electrode around a nerve for recording or stimulation.
Optic fiber implant: Implanting an optical fiber into brain tissue for optogenetic light delivery or collection.
Prism implant: Implanting a prism to redirect light paths for optical imaging experiments.
Reference electrode implant: Implanting a reference electrode to stabilize electrical recordings.
Silicon probe implant: Implanting silicon probes with multiple sites for high‑density neural recordings.
Single wire electrode implant: Implanting a thin wire electrode for recording or stimulation.
Temperature sensor implant: Implanting a device to monitor physiological temperature changes.
Tetrode wire electrode implant: Implanting a four‑wire (tetrode) bundle to record from nearby neurons simultaneously.
Generic implant: Flexible category for implants not covered above (e.g., sensors, optical devices, custom tools).
Injection and Infusion Procedures
Injection: Delivering pharmacological or genetic solutions directly into targeted brain areas.
Virus injection: Injecting viral vectors to introduce or manipulate genes in targeted cell populations.
Brain and Tissue Procedures
Brain extraction: Removing the brain for ex vivo processing and analysis.
Brain lesion: Creating a targeted injury to a brain region to study its function.
Brain slice: Preparing thin tissue sections for ex vivo recordings, imaging, and testing.
Cryosectioning: Sectioning frozen tissue into thin slices for histology.
Brain perfusion fixation: Preserving tissue by perfusing fixative through the circulatory system.
Tissue clearing: Chemically rendering tissue transparent for deep imaging.
Vibratome sectioning: Cutting tissue slices with a vibrating blade to preserve structure.
Endpoint Procedures (Euthanasia)
Cervical dislocation: Euthanasia by dislocation of the cervical vertebrae.
Decapitation: Euthanasia by removal of the head.
CO₂ chamber euthanasia: Euthanasia using a controlled carbon dioxide chamber.
Barbiturate injection: Euthanasia by barbiturate overdose injection.
Inhalant overdose: Euthanasia by overdose of inhalant anesthetics.
Abstract procedures
Auditory stimulation: Presenting controlled auditory stimuli to probe sensory processing and neural responses.
Behavioral tracking: Monitoring and quantifying behavior and movement during experiments.
Odor stimulation: Presenting controlled olfactory stimuli to study sensory processing and behavior.
Tactile stimulation: Applying touch or pressure stimuli to study somatosensory processing.
Visual stimulation: Presenting visual stimuli to study visual processing and neural activity.
Coordinate system options
Available coordinate system options for procedures:
| Type | Description |
|---|---|
| External XYZ Coordinates with Angles | Three-dimensional Cartesian system with absolute positions (X, Y, Z) and angles relative to an external reference point. Ideal for precise global positioning. |
| Stereotaxic Bregma-Based Absolute Coordinates | Stereotaxic coordinates using Bregma on the skull as origin. Uses AP, ML, DV coordinates and angles for precise skull-based targeting. |
| Stereotaxic Bregma-Based Surface Coordinates with Depth | Stereotaxic coordinates measuring from brain surface beneath Bregma. Uses AP, ML coordinates, depth, and rotation. Accommodates brain surface curvature. |
| Stereotaxic Lambda-Based Absolute Coordinates | Stereotaxic coordinates using Lambda on the skull as origin. Uses AP, ML, DV coordinates and angles. Alternative skull-based reference point for varied setups. |
| Stereotaxic Lambda-Based Surface Coordinates with Depth | Stereotaxic coordinates measuring from brain surface beneath Lambda. Uses AP, ML coordinates, depth, and rotation. Useful for targeting occipital brain areas. |
| Common Coordinate Framework XYZ Absolute Coordinates | Common Coordinate Framework using X, Y, Z absolute positions and angles. |
A detailed description of the coordinate systems can be found on the Coordinate systems page.
Permissions
Procedures inherit permissions through the subject associated with them.
Visit the permissions page to learn more.
API access
The API allows for programmable access to procedures. Learn more about the procedures’ fields and data structure on the Procedures API page.