Specimen_procedures

Model definitions

HCRSeries

Description of series of HCR staining rounds for mFISH

Field	Type	Title (Description)
codebook_name	str	Codebook name
number_of_rounds	int	Number of round
hcr_rounds	List[HybridizationChainReaction]	Hybridization Chain Reaction rounds
strip_qc_compatible	bool	Strip QC compatible
cell_id	Optional[str]	Cell ID

HybridizationChainReaction

Description of an HCR staining round

Field	Type	Title (Description)
round_index	int	Round index
start_time	datetime (timezone-aware)	Round start time
end_time	datetime (timezone-aware)	Round end time
stains	List[FluorescentStain]	Stains
probe_concentration	float	Probe concentration (M)
probe_concentration_unit	str	Probe concentration unit

PlanarSection

Description of a single planar section of brain tissue

Field	Type	Title (Description)
coordinate_system_name	str	Coordinate system name
start_coordinate	Translation	Start coordinate
end_coordinate	Optional[Translation]	End coordinate
thickness	Optional[float]	Slice thickness
thickness_unit	Optional[SizeUnit]	Slice thickness unit
partial_slice	Optional[List[AnatomicalRelative]]	Partial slice (If sectioning does not include the entire slice, indicate which part of the slice is retained.)
output_specimen_id	str	Specimen ID (Output IDs should generally follow the format {input_specimen_id}_###)
targeted_structure	Optional[BrainAtlas]	Targeted structure
includes_surrounding_tissue	Optional[bool]	Includes surrounding tissue (Whether the section includes additional tissue surrounding the targeted structure.)

PlanarSectioning

Description of a sectioning procedure performed on the coronal, sagittal, or transverse/axial plane

Field	Type	Title (Description)
coordinate_system	CoordinateSystem or Atlas or NoneType	Sectioning coordinate system (Only required if different from the Procedures.coordinate_system)
sections	List[Section or PlanarSection]	Planar sections (Use PlanarSection for new implementations)
section_orientation	SectionOrientation	Sectioning orientation

Section

Description of a single section of brain tissue. Slices should use PlanarSection.

Field	Type	Title (Description)
output_specimen_id	str	Specimen ID (Output IDs should generally follow the format {input_specimen_id}_###)
targeted_structure	Optional[BrainAtlas]	Targeted structure
includes_surrounding_tissue	Optional[bool]	Includes surrounding tissue (Whether the section includes additional tissue surrounding the targeted structure.)
coordinate_system_name	Optional[str]	[DEPRECATED] Use PlanarSection instead. Coordinate system name
start_coordinate	Optional[Translation]	[DEPRECATED] Use PlanarSection instead. Start coordinate
end_coordinate	Optional[Translation]	[DEPRECATED] Use PlanarSection instead. End coordinate
thickness	Optional[float]	[DEPRECATED] Use PlanarSection instead. Slice thickness
thickness_unit	Optional[SizeUnit]	[DEPRECATED] Use PlanarSection instead. Slice thickness unit
partial_slice	Optional[List[AnatomicalRelative]]	[DEPRECATED] Use PlanarSection instead. Partial slice (If sectioning does not include the entire slice, indicate which part of the slice is retained.)

SectionOrientation

Orientation of sectioning

Name	Value
CORONAL	Coronal
SAGITTAL	Sagittal
TRANSVERSE	Transverse

Sectioning

Description of a sectioning procedure targeting a specific structure

Field	Type	Title (Description)
sections	List[Section]	Sections

SpecimenProcedure

Description of surgical or other procedure performed on a specimen

Field	Type	Title (Description)
procedure_type	SpecimenProcedureType	Procedure type
procedure_name	Optional[str]	Procedure name
specimen_id	str or List[str]	Specimen ID(s)
start_date	datetime.date	Start date
end_date	datetime.date	End date
experimenters	List[str]	experimenter(s)
protocol_parameters	Optional[Dict[str, str]]	Protocol parameters (Parameters defined in the protocol and their value during this procedure)
procedure_details	List[HCRSeries or FluorescentStain or Sectioning or PlanarSectioning or ProbeReagent or Reagent or GeneProbeSet or Solution]	Procedure details (Details of the procedures, including reagents and sectioning information.)
notes	Optional[str]	Notes
protocol_id	Optional[List[str]]	Protocol ID (DOI for protocols.io)