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 | Type of procedure (required). See options below |
Subject | The subject the procedure was performed on (required) |
Notes | Notes about the procedure (max length: 500 characters) |
Date and time | Date and time the procedure was performed (e.g., “2023-03-22”) |
Consumable | Consumable used for the procedure |
Hardware device | Hardware device used to perform the procedure |
Brain region | Target brain region where the procedure was performed |
Coordinates system | Coordinate system (required). See options below |
Type details | Type-specific fields. See options below |
Types of procedures
These are the available Type options for Procedure:
- Brain lesion
- Craniectomy
- Craniotomy
- Optic fiber implant
- Brain perfusion fixation
- Single wire electrode
- Silicon probe implant
- Brain slice
- Tetrode wire electrode
- Virus injection
A detailed list of the type-specific fields can be found on the procedure types page.
Coordinate system options
Available Coordinate system options for Procedure:
| Type | Description |
|---|---|
External X-Y-Z 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 | 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 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 | 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 with Depth | Stereotaxic coordinates measuring from brain surface beneath Lambda. Uses AP, ML coordinates, depth, and rotation. Useful for targeting occipital brain areas. |
Stereotaxic X-Y-Z Absolute | Stereotaxic coordinates using X, Y, Z absolute positions and angles. Enables precise navigation within stereotaxic frame. |
Stereotaxic X-Y Surface with Depth | Stereotaxic coordinates using X, Y positions on brain surface, plus depth and rotation. For experiments needing lateral and anteroposterior precision. |
A detailed list of the fields in Coordinate system can be found on the Coordinate system page.
Permissions
Procedures inherit permissions through the subject associated with them.
Visit the permissions page to learn more.
Procedure API access
The API allows for programmable access to procedures. Learn more about the procedures’ fields and data structure on the Procedure API page.