Procedures

Link to code

The procedures.json file contains anything done to the subject or specimen prior to data collection. This can include surgeries, injections, tissue processing, sectioning, immunolabeling, etc. The procedures metadata also contains implanted devices and their configurations, for example for chronic insertions.

Subject procedure vs. specimen procedure

Subject procedures are performed on a live subject (e.g. injections, surgeries, implants, perfusions, etc.) whereas specimen procedures are performed on tissue extracted after perfusion (e.g. tissue processing, immunolabeling, sectioning, etc.).

Sectioned specimens must have a unique number appended as a suffix to the subject ID: <subject_id>_<###>.

Examples

• Generic procedures

• SmartSPIM procedures

• Ophys procedures

Core file

Procedures

Description of all procedures performed on a subject, including surgeries, injections, and tissue processing

Field	Type	Description
subject_id	str	Unique identifier for the subject of data acquisition
subject_procedures	List[Surgery or Injection or TrainingProtocol or WaterRestriction or GenericSubjectProcedure]	Procedures performed on a live subject
specimen_procedures	List[SpecimenProcedure]	Procedures performed on tissue extracted after perfusion
coordinate_system	Optional[CoordinateSystem]	Origin and axis definitions for determining the configured position of devices implanted during procedures. Required when coordinates are provided within the Procedures
notes	Optional[str]