| Package | Description |
|---|---|
| sc.fiji.snt |
SNT core classes
|
| sc.fiji.snt.analysis |
Analysis of
Trees. |
| sc.fiji.snt.analysis.graph |
Classes for handling neuronal reconstructions as graphs
|
| sc.fiji.snt.annotation |
Classes handling neuropil annotations and atlases metadata.
|
| sc.fiji.snt.util |
Miscellaneous SNT utilities, including classes defining reconstruction nodes.
|
| sc.fiji.snt.viewer.geditor |
| Modifier and Type | Method and Description |
|---|---|
BrainAnnotation |
Path.getNodeAnnotation(int pos)
Returns the neuropil annotation associated with this node.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Path.setNodeAnnotation(BrainAnnotation annotation,
int pos)
Assigns an annotation to an existing node.
|
| Modifier and Type | Method and Description |
|---|---|
Map<BrainAnnotation,Integer> |
NodeStatistics.getAnnotatedFrequencies()
Retrieves the count frequencies across brain compartment.
|
Map<BrainAnnotation,Integer> |
NodeStatistics.getAnnotatedFrequencies(int level)
Retrieves the count frequencies across brain compartment.
|
Map<BrainAnnotation,Integer> |
NodeStatistics.getAnnotatedFrequencies(int level,
String hemisphere)
Retrieves the count frequencies across brain compartment.
|
Map<BrainAnnotation,int[]> |
NodeStatistics.getAnnotatedFrequenciesByHemisphere(int level,
Tree tree) |
protected static Map<BrainAnnotation,Double> |
TreeStatistics.getAnnotatedLength(DirectedWeightedGraph graph,
int level,
char lr) |
Map<BrainAnnotation,Double> |
TreeStatistics.getAnnotatedLength(int level)
Retrieves the amount of cable length present on each brain compartment
innervated by the analyzed neuron.
|
Map<BrainAnnotation,Double> |
MultiTreeStatistics.getAnnotatedLength(int level) |
Map<BrainAnnotation,Double> |
TreeStatistics.getAnnotatedLength(int level,
String hemisphere)
Retrieves the amount of cable length present on each brain compartment
innervated by the analyzed neuron.
|
Map<BrainAnnotation,Double> |
MultiTreeStatistics.getAnnotatedLength(int level,
String hemisphere) |
protected static Map<BrainAnnotation,double[]> |
TreeStatistics.getAnnotatedLengthsByHemisphere(DirectedWeightedGraph graph,
int level) |
Map<BrainAnnotation,double[]> |
TreeStatistics.getAnnotatedLengthsByHemisphere(int level) |
Map<BrainAnnotation,double[]> |
MultiTreeStatistics.getAnnotatedLengthsByHemisphere(int level) |
Map<BrainAnnotation,Set<T>> |
NodeStatistics.getAnnotatedNodes()
Splits the nodes being analyzed into groups sharing the same brain
annotation.
|
Map<BrainAnnotation,Set<T>> |
NodeStatistics.getAnnotatedNodes(int level)
Splits the nodes being analyzed into groups sharing the same brain
annotation.
|
Set<BrainAnnotation> |
TreeAnalyzer.getAnnotations() |
Set<BrainAnnotation> |
MultiTreeStatistics.getAnnotations() |
Set<BrainAnnotation> |
TreeAnalyzer.getAnnotations(int level) |
Set<BrainAnnotation> |
MultiTreeStatistics.getAnnotations(int level) |
| Modifier and Type | Method and Description |
|---|---|
List<T> |
NodeStatistics.get(BrainAnnotation compartment)
Gets the list of nodes associated with the specified compartment (neuropil
label).
|
List<T> |
NodeStatistics.get(BrainAnnotation compartment,
boolean includeChildren)
Gets the list of nodes associated with the specified compartment (neuropil
label).
|
Set<PointInImage> |
TreeAnalyzer.getBranchPoints(BrainAnnotation annot)
Gets the position of all the branch points in the analyzed tree associated
with the specified annotation.
|
double |
TreeAnalyzer.getCableLength(BrainAnnotation compartment)
Gets the cable length associated with the specified compartment (neuropil
label).
|
double |
MultiTreeStatistics.getCableLength(BrainAnnotation compartment) |
double |
TreeAnalyzer.getCableLength(BrainAnnotation compartment,
boolean includeChildren)
Gets the cable length associated with the specified compartment (neuropil
label).
|
double |
TreeAnalyzer.getCableLengthNorm(BrainAnnotation compartment)
Gets the cable length associated with the specified compartment (neuropil
label) as a ratio of total length.
|
int |
TreeAnalyzer.getNbranchPoints(BrainAnnotation annot)
Gets the number of branch points in the analyzed tree associated with the
specified annotation.
|
double |
TreeAnalyzer.getNbranchPointsNorm(BrainAnnotation annot)
Gets the percentage of branch points in the analyzed tree associated with the
specified annotation
|
int |
TreeAnalyzer.getNtips(BrainAnnotation annot)
Gets the number of end points in the analyzed tree associated with the
specified annotation.
|
double |
TreeAnalyzer.getNtipsNorm(BrainAnnotation annot)
Gets the percentage of end points in the analyzed tree associated with the
specified annotation
|
Set<PointInImage> |
TreeAnalyzer.getTips(BrainAnnotation annot)
Gets the position of all the tips in the analyzed tree associated with the
specified annotation.
|
protected boolean |
TreeAnalyzer.isSameOrParentAnnotation(BrainAnnotation annot,
BrainAnnotation annotToBeTested) |
| Modifier and Type | Method and Description |
|---|---|
protected SNTChart |
TreeStatistics.getAnnotatedLengthHistogram(Map<BrainAnnotation,Double> map,
int depth,
String secondaryLabel) |
SNTChart |
GroupedTreeStatistics.getBoxPlot(String feature,
Collection<BrainAnnotation> annotations)
Assembles a Box and Whisker Plot for the specified feature (absolute
measurements).
|
SNTChart |
GroupedTreeStatistics.getBoxPlot(String feature,
Collection<BrainAnnotation> annotations,
double cutoff,
boolean normalize)
Assembles a Box and Whisker Plot for the specified feature.
|
| Modifier and Type | Method and Description |
|---|---|
BrainAnnotation |
AnnotationWeightedEdge.getSource() |
BrainAnnotation |
AnnotationWeightedEdge.getTarget() |
| Modifier and Type | Method and Description |
|---|---|
Set<BrainAnnotation> |
AnnotationGraph.removeOrphans() |
| Modifier and Type | Class and Description |
|---|---|
class |
AllenCompartment
Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate
Framework] annotation.
|
class |
InsectBrainCompartment |
| Modifier and Type | Method and Description |
|---|---|
BrainAnnotation |
InsectBrainCompartment.getAncestor(int level) |
BrainAnnotation |
BrainAnnotation.getAncestor(int level) |
BrainAnnotation |
InsectBrainCompartment.getParent() |
BrainAnnotation |
BrainAnnotation.getParent() |
| Modifier and Type | Method and Description |
|---|---|
boolean |
InsectBrainCompartment.isChildOf(BrainAnnotation annotation) |
boolean |
BrainAnnotation.isChildOf(BrainAnnotation annotation) |
boolean |
AllenCompartment.isChildOf(BrainAnnotation childCompartment)
Assesses if this annotation is a child of a specified compartment.
|
boolean |
InsectBrainCompartment.isParentOf(BrainAnnotation parentCompartment) |
boolean |
BrainAnnotation.isParentOf(BrainAnnotation parentCompartment) |
boolean |
AllenCompartment.isParentOf(BrainAnnotation childCompartment)
Assesses if this annotation is the parent of the specified compartment.
|
protected void |
InsectBrainCompartment.setParent(BrainAnnotation parent) |
| Modifier and Type | Method and Description |
|---|---|
BrainAnnotation |
SWCPoint.getAnnotation() |
BrainAnnotation |
SNTPoint.getAnnotation() |
BrainAnnotation |
PointInImage.getAnnotation() |
| Modifier and Type | Method and Description |
|---|---|
void |
SWCPoint.setAnnotation(BrainAnnotation annotation) |
void |
SNTPoint.setAnnotation(BrainAnnotation annotation)
Assigns a neuropil annotation (e.g., atlas compartment) to this point.
|
void |
PointInImage.setAnnotation(BrainAnnotation annotation) |
| Modifier and Type | Method and Description |
|---|---|
void |
AnnotationGraphAdapter.setVertexColor(BrainAnnotation vertex,
ColorRGB color) |
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