Specimen_procedures

Model definitions

HCRSeries

Description of series of HCR staining rounds for mFISH

Field	Type	Description
codebook_name	str
number_of_rounds	int
hcr_rounds	List[HybridizationChainReaction]
strip_qc_compatible	bool
cell_id	Optional[str]

HybridizationChainReaction

Description of an HCR staining round

Field	Type	Description
round_index	int
start_time	datetime (timezone-aware)
end_time	datetime (timezone-aware)
stains	List[FluorescentStain]
probe_concentration	float
probe_concentration_unit	str

PlanarSectioning

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

Field	Type	Description
coordinate_system	Optional[CoordinateSystem]	Only required if different from the Procedures.coordinate_system
sections	List[Section]
section_orientation	SectionOrientation

Section

Description of a slice of brain tissue

Field	Type	Description
output_specimen_id	str
targeted_structure	Optional[BrainAtlas]
coordinate_system_name	str
start_coordinate	Translation
end_coordinate	Optional[Translation]
thickness	Optional[float]
thickness_unit	Optional[SizeUnit]
partial_slice	Optional[List[AnatomicalRelative]]	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

SpecimenProcedure

Description of surgical or other procedure performed on a specimen

Field	Type	Description
procedure_type	SpecimenProcedureType
procedure_name	Optional[str]
specimen_id	str
start_date	datetime.date
end_date	datetime.date
experimenters	List[Person]
protocol_id	Optional[List[str]]	DOI for protocols.io
protocol_parameters	Optional[Dict[str, str]]	Parameters defined in the protocol and their value during this procedure
procedure_details	List[HCRSeries or FluorescentStain or PlanarSectioning or ProbeReagent or Reagent or GeneProbeSet]	Details of the procedures, including reagents and sectioning information.
notes	Optional[str]