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Procedure model

Table of contents

  1. Introduction
  2. Fields
  3. Types of procedures
    1. Surgical Procedures
    2. Implant Procedures
    3. Brain and Tissue Procedures
    4. Injection and Infusion Procedures
  4. Coordinate system options
  5. Permissions
  6. Procedure API access

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

FieldDescription
TypeType of procedure (required). Selected from predefined types. Example: “Optic fiber implant”. See options below
SubjectThe subject the procedure was performed on (required). Must reference an existing subject. Example: “Mouse_01”
NotesNotes about the procedure (string). Example: “Implant placed successfully with minimal bleeding”
Date and timeDate and time the procedure was performed. Example: “2024-03-22 10:30:00”
ConsumableConsumable used for the procedure. Example: “200µm core diameter fiber”
Hardware deviceHardware device used to perform the procedure. Example: “Stereotaxic frame #3”
Brain regionTarget brain region where the procedure was performed. Example: “Hippocampus CA1”
Coordinates systemCoordinate system (required). Selected from predefined systems. Example: “Stereotaxic Bregma-Based”. See options below
Type detailsType-specific fields. Fields vary by procedure type. Example: For fiber implant - fiber tip shape. See options below

Types of procedures

These are the available Type options for Procedure:

Surgical Procedures

  • Craniectomy
  • Craniotomy

Implant Procedures

  • Optic fiber implant
  • Silicon probe implant
  • Single wire electrode
  • Tetrode wire electrode

Brain and Tissue Procedures

  • Brain lesion
  • Brain perfusion fixation
  • Brain slice

Injection and Infusion Procedures

  • 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:

TypeDescription
External X-Y-Z Coordinates with AnglesThree-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 AbsoluteStereotaxic 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 DepthStereotaxic coordinates measuring from brain surface beneath Bregma. Uses AP, ML coordinates, depth, and rotation. Accommodates brain surface curvature.
Stereotaxic Lambda-Based AbsoluteStereotaxic 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 DepthStereotaxic coordinates measuring from brain surface beneath Lambda. Uses AP, ML coordinates, depth, and rotation. Useful for targeting occipital brain areas.
Stereotaxic X-Y-Z AbsoluteStereotaxic coordinates using X, Y, Z absolute positions and angles. Enables precise navigation within stereotaxic frame.
Stereotaxic X-Y Surface with DepthStereotaxic 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.