surgery_procedures.md

Surgery_procedures

Model definitions

Anaesthetic

Description of an anaesthetic

Field	Type	Title (Description)
anaesthetic_type	str	Type
duration	float	Duration
duration_unit	TimeUnit	Duration unit
level	Optional[float]	Level (percent)

BrainInjection

Description of an injection procedure into a brain

Field	Type	Title (Description)
coordinate_system_name	str	Coordinate system name
coordinates	List[List[Translation or Rotation or Scale or Affine]]	Injection coordinate, depth, and rotation
targeted_structure	Optional[BrainAtlas]	Injection targeted brain structure
injection_materials	List[ViralMaterial or NonViralMaterial]	Injection material
relative_position	Optional[List[AnatomicalRelative]]	Relative position
dynamics	List[InjectionDynamics]	Injection dynamics (List of injection events, one per location/depth)
protocol_id	Optional[str]	[DEPRECATED] Use protocol_id in Surgery or NonSurgicalInjection instead. Protocol ID (DOI for protocols.io)

CatheterImplant

Description of a catheter implant procedure

Field	Type	Title (Description)
where_performed	Organization	Where performed
implanted_device	Catheter	Implanted device
device_config	CatheterConfig	Device configuration

Craniotomy

Description of craniotomy procedure

Field	Type	Title (Description)
protocol_id	Optional[str]	Protocol ID (DOI for protocols.io)
craniotomy_type	CraniotomyType	Craniotomy type
coordinate_system_name	Optional[str]	Coordinate system name
position	Translation or List[AnatomicalRelative] or NoneType	Craniotomy position
size	Optional[float]	Craniotomy size (Diameter or side length)
size_unit	Optional[SizeUnit]	Craniotomy size unit
protective_material	Optional[ProtectiveMaterial]	Protective material
implant_part_number	Optional[str]	Implant part number
dura_removed	Optional[bool]	Dura removed

CraniotomyType

Name of craniotomy Type

Name	Value
DHC	Dual hemisphere craniotomy
WHC	Whole hemisphere craniotomy
CIRCLE	Circle
SQUARE	Square
OTHER	Other

GenericSurgeryProcedure

Description of a surgery procedure performed on a subject

Field	Type	Title (Description)
protocol_id	Optional[str]	Protocol ID (DOI for protocols.io)
description	str	Description
notes	Optional[str]	Notes

GroundWireImplant

Ground wire implant procedure

Field	Type	Title (Description)
ground_electrode_location	MouseAnatomyModel	Location of ground electrode
ground_wire_hole	Optional[int]	Ground wire hole (For SHIELD implants, the hole number for the ground wire)
ground_wire_material	Optional[GroundWireMaterial]	Ground wire material
ground_wire_diameter	Optional[float]	Ground wire diameter
ground_wire_diameter_unit	Optional[SizeUnit]	Ground wire diameter unit

GroundWireMaterial

Ground wire material name

Name	Value
SILVER	Silver
PLATINUM_IRIDIUM	Platinum iridium

Headframe

Description of headframe procedure

Field	Type	Title (Description)
protocol_id	Optional[str]	Protocol ID (DOI for protocols.io)
headframe_type	str	Headframe type
headframe_part_number	Optional[str]	Headframe part number
headframe_material	Optional[HeadframeMaterial]	Headframe material
well_part_number	Optional[str]	Well part number
well_type	Optional[str]	Well type

HeadframeMaterial

Headframe material name

Name	Value
STEEL	Steel
TITANIUM	Titanium
WHITE_ZIRCONIA	White Zirconia

MyomatrixInsertion

Description of a Myomatrix array insertion for EMG

Field	Type	Title (Description)
protocol_id	Optional[str]	Protocol ID (DOI for protocols.io)
ground_electrode	GroundWireImplant	Ground electrode
implanted_device	MyomatrixArray	Implanted device

Perfusion

Description of a perfusion procedure that creates a specimen

Field	Type	Title (Description)
protocol_id	Optional[str]	Protocol ID (DOI for protocols.io)
output_specimen_ids	List[str]	Specimen ID (IDs of specimens resulting from this procedure.)

ProbeImplant

Description of a probe (fiber, ephys) implant procedure

Field	Type	Title (Description)
protocol_id	Optional[str]	Protocol ID (DOI for protocols.io)
implanted_device	EphysProbe or FiberProbe	Implanted device
device_config	ProbeConfig	Device configuration

ProtectiveMaterial

Name of material applied to craniotomy

Name	Value
AGAROSE	Agarose
DURAGEL	Duragel
KWIK_CAST	Kwik-Cast
SORTA_CLEAR	SORTA-clear
OTHER	Other - see notes

SampleCollection

Description of a single sample collection

Field	Type	Title (Description)
sample_type	SampleType	Sample type
time	datetime (timezone-aware)	Collection time
collection_volume	float	Collection volume
collection_volume_unit	VolumeUnit	Collection volume unit
collection_method	Optional[str]	Collection method for terminal collection

SampleType

Sample type

Name	Value
BLOOD	Blood
OTHER	Other