Uses of Class
sc.fiji.snt.annotation.AllenCompartment

Packages that use AllenCompartment

Package	Description
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.annotation	Classes handling neuropil annotations and atlases metadata.
sc.fiji.snt.io	Classes for importing reconstructions into SNT.

Uses of AllenCompartment in sc.fiji.snt.analysis

Methods in sc.fiji.snt.analysis with parameters of type AllenCompartment

Modifier and Type	Method	Description
void	MultiTreeColorMapper.mapRootDistanceToCentroid(AllenCompartment compartment, net.imglib2.display.ColorTable colorTable)

Uses of AllenCompartment in sc.fiji.snt.annotation

Methods in sc.fiji.snt.annotation that return AllenCompartment

Modifier and Type	Method	Description
AllenCompartment	AllenCompartment.getAncestor(int level)	Gets the nth ancestor of this compartment.
static AllenCompartment	AllenUtils.getCompartment(int id)	Constructs a compartment from its CCF id
static AllenCompartment	AllenUtils.getCompartment(String nameOrAcronym)	Constructs a compartment from its CCF name or acronym
AllenCompartment	AllenCompartment.getParent()	Gets the parent of this compartment.

Methods in sc.fiji.snt.annotation that return types with arguments of type AllenCompartment

Modifier and Type	Method	Description
List<AllenCompartment>	AllenCompartment.getAncestors()	Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.
List<AllenCompartment>	AllenCompartment.getChildren()	Gets the child ontologies of this compartment as a flat (non-hierarchical) list.
List<AllenCompartment>	AllenCompartment.getChildren(int level)	Gets the child ontologies of this compartment as a flat (non-hierarchical) list.
static List<AllenCompartment>	AllenUtils.getOntologies()	Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.
static List<AllenCompartment>	AllenUtils.getOntologies(int depth, boolean meshes)	Gets a flat (non-hierarchical) list of all the compartments of the specified ontology depth.
List<AllenCompartment>	AllenCompartment.getTreePath()	Gets the tree path of this compartment.

Uses of AllenCompartment in sc.fiji.snt.io

Methods in sc.fiji.snt.io that return AllenCompartment

Modifier and Type	Method	Description
AllenCompartment	MouseLightLoader.getSomaCompartment()	Gets the brain compartment containing the soma.

Methods in sc.fiji.snt.io with parameters of type AllenCompartment

Modifier and Type	Method	Description
static List<String>	MouseLightQuerier.getIDs(AllenCompartment compartment)	Gets neuron IDs for the specified brain compartment.

Method parameters in sc.fiji.snt.io with type arguments of type AllenCompartment

Modifier and Type	Method	Description
static List<String>	MouseLightQuerier.getIDs(Collection<AllenCompartment> compartments)	Gets neuron IDs for the specified collection of brain compartments.