Surgery_procedures¶

Model definitions¶

Anaesthetic¶

Description of an anaesthetic

Field	Type	Description
`anaesthetic_type`	`str`
`duration`	`float`
`duration_unit`	TimeUnit
`level`	`Optional[float]`

BrainInjection¶

Description of an injection procedure into a brain

Field	Type	Description
`coordinate_system_name`	`str`
`coordinates`	List[List[Translation or Rotation or Scale or Affine]]
`targeted_structure`	Optional[BrainAtlas]
`injection_materials`	List[ViralMaterial or NonViralMaterial]
`relative_position`	Optional[List[AnatomicalRelative]]
`dynamics`	List[InjectionDynamics]	List of injection events, one per location/depth
`protocol_id`	`Optional[str]`	DOI for protocols.io

CatheterImplant¶

Description of a catheter implant procedure

Field	Type	Description
`where_performed`	Organization
`implanted_device`	Catheter
`device_config`	CatheterConfig

Craniotomy¶

Description of craniotomy procedure

Field	Type	Description
`protocol_id`	`Optional[str]`	DOI for protocols.io
`craniotomy_type`	CraniotomyType
`coordinate_system_name`	`Optional[str]`
`position`	Translation or List[AnatomicalRelative] or NoneType
`size`	`Optional[float]`	Diameter or side length
`size_unit`	Optional[SizeUnit]
`protective_material`	Optional[ProtectiveMaterial]
`implant_part_number`	`Optional[str]`
`dura_removed`	`Optional[bool]`

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	Description
`protocol_id`	`Optional[str]`	DOI for protocols.io
`description`	`str`
`notes`	`Optional[str]`

GroundWireImplant¶

Ground wire implant procedure

Field	Type	Description
`ground_electrode_location`	MouseAnatomyModel
`ground_wire_hole`	`Optional[int]`	For SHIELD implants, the hole number for the ground wire
`ground_wire_material`	Optional[GroundWireMaterial]
`ground_wire_diameter`	`Optional[float]`
`ground_wire_diameter_unit`	Optional[SizeUnit]

GroundWireMaterial¶

Ground wire material name

Name	Value
`SILVER`	`Silver`
`PLATINUM_IRIDIUM`	`Platinum iridium`

Headframe¶

Description of headframe procedure

Field	Type	Description
`protocol_id`	`Optional[str]`	DOI for protocols.io
`headframe_type`	`str`
`headframe_part_number`	`str`
`headframe_material`	Optional[HeadframeMaterial]
`well_part_number`	`Optional[str]`
`well_type`	`Optional[str]`

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	Description
`protocol_id`	`Optional[str]`	DOI for protocols.io
`ground_electrode`	GroundWireImplant
`implanted_device`	MyomatrixArray

Perfusion¶

Description of a perfusion procedure that creates a specimen

Field	Type	Description
`protocol_id`	`Optional[str]`	DOI for protocols.io
`output_specimen_ids`	`List[str]`	IDs of specimens resulting from this procedure.

ProbeImplant¶

Description of a probe (fiber, ephys) implant procedure

Field	Type	Description
`protocol_id`	`Optional[str]`	DOI for protocols.io
`implanted_device`	EphysProbe or FiberProbe
`device_config`	ProbeConfig

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	Description
`sample_type`	SampleType
`time`	`datetime (timezone-aware)`
`collection_volume`	`float`
`collection_volume_unit`	VolumeUnit
`collection_method`	`Optional[str]`

SampleType¶

Sample type

Name	Value
`BLOOD`	`Blood`
`OTHER`	`Other`