openminds.v5.specimen_prep

In-depth metadata for the preparation of specimens (e.g. cell culture, surgical procedures, tissue slicing).

class CranialWindowPreparation(lookup_label=None, construction_type=None, custom_property_sets=None, description=None, dimension=None, end_time=None, inputs=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, reinforcement_type=None, start_time=None, study_targets=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, CranialWindowPreparation

<description not available>

Parameters:

• construction_type (CranialWindowConstructionType) – no description available

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the cranial window preparation.

• dimension (CentroidalPyramid, Circle, CircularSector, Cube, Ellipse, Ellipsoid, EquilateralTriangle, Frustum, IsoscelesTriangle, Kite, Parallelogram, Rectangle, RegularPolygon, Rhombus, RightCone, RightCylinder, RightPrism, RightTriangle, Sphere, Spheroid, Square, Trapezoid, Triangle) – no description available

• end_time (datetime, time) – no description available

• inputs (SubjectState) – Something or someone that is put into or participates in a process or machine.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (SubjectState) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• reinforcement_type (CranialWindowReinforcementType) – no description available

• start_time (datetime, time) – no description available

• study_targets (AnatomicalCavity, AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, DeviceType, Disease, DiseaseModel, ElectricalStimulusType, ExternalBodyRegion, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, TissueStructure, VascularStructure, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class TissueCulturePreparation(lookup_label=None, culture_medium=None, culture_type=None, custom_property_sets=None, description=None, end_time=None, inputs=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, start_time=None, study_targets=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, TissueCulturePreparation

<description not available>

Parameters:

• culture_medium (ChemicalMixture) – no description available

• culture_type (CellCultureType) – no description available

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the tissue culture preparation.

• end_time (datetime, time) – no description available

• inputs (TissueSampleState, TissueSampleCollectionState, SubjectGroupState, SubjectState) – Something or someone that is put into or participates in a process or machine.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (TissueSampleState) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• start_time (datetime, time) – no description available

• study_targets (AnatomicalCavity, AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, DeviceType, Disease, DiseaseModel, ElectricalStimulusType, ExternalBodyRegion, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, TissueStructure, VascularStructure, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class TissueSampleSlicing(lookup_label=None, custom_property_sets=None, description=None, device=None, end_time=None, inputs=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, start_time=None, study_targets=None, temperature=None, tissue_bath_solution=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, TissueSampleSlicing

<description not available>

Parameters:

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the tissue sample slicing.

• device (SlicingDeviceUsage) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• end_time (datetime, time) – no description available

• inputs (SubjectState, TissueSampleCollectionState, TissueSampleState) – Something or someone that is put into or participates in a process or machine.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (TissueSampleCollectionState, TissueSampleState) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• start_time (datetime, time) – no description available

• study_targets (AnatomicalCavity, AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, DeviceType, Disease, DiseaseModel, ElectricalStimulusType, ExternalBodyRegion, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, TissueStructure, VascularStructure, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

• temperature (QuantitativeValue, QuantitativeValueRange) – no description available

• tissue_bath_solution (ChemicalMixture) – no description available

class SlicingDevice(name=None, contributions=None, description=None, internal_identifier=None, is_part_of=None, serial_number=None, type=None, usage=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, SlicingDevice

<description not available>

Parameters:

• contributions (Organization, Person) – no description available

• description (str) – Longer statement or account giving the characteristics of the slicing device.

• internal_identifier (str) – Term or code that identifies the slicing device within a particular product.

• name (str) – Word or phrase that constitutes the distinctive designation of the slicing device.

• serial_number (str) – no description available

• type (DeviceType, HardwareProduct) – Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.

• is_part_of (Setup) – reverse of ‘has_parts’

• usage (SlicingDeviceUsage) – reverse of ‘device’

class SlicingDeviceUsage(lookup_label=None, device=None, generation_device=None, is_used_to_obtain=None, metadata_locations=None, oscillation_amplitude=None, placed_by=None, slice_thickness=None, slicing_angles=None, slicing_plane=None, slicing_speed=None, used_for=None, used_in=None, used_specimen=None, vibration_frequency=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, SlicingDeviceUsage

<description not available>

Parameters:

• device (SlicingDevice) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• lookup_label (str) – no description available

• metadata_locations (File, FileBundle) – no description available

• oscillation_amplitude (QuantitativeValue) – no description available

• slice_thickness (QuantitativeValue, QuantitativeValueRange) – no description available

• slicing_angles (QuantitativeValue, NumericalProperty) – no description available

• slicing_plane (AnatomicalPlane) – no description available

• slicing_speed (QuantitativeValue) – no description available

• used_specimen (SubjectState, TissueSampleState) – no description available

• vibration_frequency (QuantitativeValue) – no description available

• generation_device (EphysStimulus) – reverse of ‘generated_by’

• is_used_to_obtain (GridImage, GridImageSequence, GridImageStack, GridVolume, GridVolumeSequence, Measurement, RegularTimeSeries) – reverse of ‘obtained_with’

• placed_by (ElectrodePlacement) – reverse of ‘devices’

• used_for (TissueSampleSlicing) – reverse of ‘device’

• used_in (CellPatching) – reverse of ‘devices’