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)
global_coordinate_system	CoordinateSystem or Atlas or NoneType	Sectioning global coordinate system (Only required if different from the Procedures.global_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.)

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 FluorescentReagent 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)