Procedures¶
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.).
SpecimenProcedure.specimen_id¶
After perfusion or death we refer to specimens by the specimen_id field. When the tissue has not been sectioned in some way the specimen_id should be identical to the subject_id. Sectioned specimens should have a unique number appended as a suffix to the subject ID: <subject_id>_<###>.
Examples¶
Core file¶
Procedures¶
Description of all procedures performed on a subject, including surgeries, injections, and tissue processing
Field |
Type |
Title (Description) |
|---|---|---|
|
|
Subject ID (Unique identifier for the subject of data acquisition) |
|
List[Surgery or Injection or NonSurgicalInjection or TrainingProtocol or WaterRestriction or GenericSubjectProcedure] |
Subject Procedures (Procedures performed on a live subject) |
|
List[SpecimenProcedure] |
Specimen Procedures (Procedures performed on tissue extracted after perfusion) |
|
Optional[CoordinateSystem] |
Coordinate System (Origin and axis definitions for determining the configured position of devices implanted during procedures. Required when coordinates are provided within the Procedures) |
|
|
Notes |