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]`	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)
`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
`protocol_id`	`Optional[str]`	Protocol ID (DOI for protocols.io)

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

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)
`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
`protocol_id`	`Optional[str]`	Protocol ID (DOI for protocols.io)

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

Perfusion¶

Description of a perfusion procedure that creates a specimen

Field	Type	Title (Description)
`output_specimen_ids`	`List[str]`	Specimen ID (IDs of specimens resulting from this procedure. Whole brains can use the {subject_id}, partial sections should always include a suffix {subject_id}_###)
`protocol_id`	`Optional[str]`	Protocol ID (DOI for protocols.io)

ProbeImplant¶

Description of a probe (fiber, ephys) implant procedure

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

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`