AllenUtils Class Documentation#
Package: sc.fiji.snt.annotation
Utility methods for accessing/handling AllenCompartments
Methods#
Getters Methods#
- static getAnatomicalPlane(String)
Retrieves the anatomical plane matching the specified cartesian plane.
- static getAxisDefiningSagittalPlane()
Gets the axis defining the sagittal plane.
- static getCartesianPlane(String)
Retrieves the Cartesian plane matching the specified anatomical plane.
- static getCompartment(String)
Constructs a compartment from its CCF name or acronym
- static getHemisphere(Tree)
Checks the hemisphere a neuron belongs to.
- static getHighestOntologyDepth()
Gets the maximum number of ontology levels in the Allen CCF.
- static getOntologies()
Gets a flat (non-hierarchical) list of all the compartments of the specified ontology depth.
- static getRootMesh(ColorRGB)
Retrieves the surface contours for the Allen Mouse Brain Atlas (CCF), bundled with SNT.
- static getTreeModel(boolean)
Retrieves the Allen CCF hierarchical tree data.
- static getXYZLabels()
- static isLeftHemisphere(double, double, double)
Other Methods#
- static assignAnnotationsFromNodeValues(Tree)
Assigns brain annotations (interpreted as CCF IDs) to node values for all paths in a Tree.
This method is the inverse operation of transferAnnotationIdsToNodeValues(Tree).
- static assignHemisphereTags(DirectedWeightedGraph)
- static assignToLeftHemisphere(Tree)
Assigns a tree to the left hemisphere by mirroring it if necessary.
- static assignToRightHemisphere(Tree)
Assigns a tree to the right hemisphere by mirroring it if necessary.
- static brainCenter()
Returns the spatial centroid of the Allen CCF.
- static main(String;)
- static splitByHemisphere(DirectedWeightedGraph)
- static transferAnnotationIdsToNodeValues(Tree)
Transfers brain annotation IDs to node values for all paths in a Tree.
This is useful for preserving annotation information when saving data to TRACES files. Note that this method overwrites any existing node values. Nodes without annotations (null) are assigned BRAIN_ROOT_ID.