| 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.analysis.sholl.parsers |
Parsers to retrieve Profiles from multiple sources (2D/3D images, reconstructions, and tables)
|
| sc.fiji.snt.annotation |
Classes handling neuropil annotations and atlases metadata.
|
| sc.fiji.snt.io |
Classes for importing reconstructions into SNT.
|
| sc.fiji.snt.plugin |
SNT add-ons as IJ2 commands
|
| sc.fiji.snt.viewer |
Visualization of reconstructions
|
| Modifier and Type | Method and Description |
|---|---|
Tree |
Tree.clone() |
Tree |
SNTService.demoTree()
Deprecated.
|
Tree |
SNTService.demoTree(String tree)
Returns a demo tree.
|
static Tree |
Tree.fromFile(String filePath)
Script-friendly method for creating a Tree from a reconstruction file.
|
Tree |
PathManagerUI.geSelectedPathsAsTree()
Gets the collection of paths listed in the Path Manager as a
Tree
object. |
protected Tree |
PathManagerUI.getMultipleTreesInASingleContainer() |
protected Tree |
PathManagerUI.getSingleTree() |
Tree |
SNTService.getTree()
Gets the collection of paths listed in the Path Manager as a
Tree
object. |
Tree |
SNTService.getTree(boolean selectedPathsOnly)
Gets the collection of paths listed in the Path Manager as a
Tree
object. |
Tree |
Tree.subTree(int... swcTypes)
Extracts the subset of paths matching the specified criteria.
|
Tree |
Tree.subTree(String... swcTypes)
Extracts the subset of paths matching the specified criteria (script friendly
method)
|
| Modifier and Type | Method and Description |
|---|---|
List<Tree> |
SNTService.demoTrees()
Returns a collection of four demo reconstructions (dendrites from pyramidal
cells from the MouseLight database).
|
protected List<Tree> |
SNTService.demoTreesSWC() |
protected Collection<Tree> |
PathManagerUI.getMultipleTrees() |
Map<String,Tree> |
PathManagerUI.getSelectedPathsOrganizedByTrees(boolean ifNoneSelectedGetAll)
|
Collection<Tree> |
PathAndFillManager.getTrees()
Returns all the paths associated with this PathAndFillManager instance,
grouped by Tree.
|
Map<String,Tree> |
PathAndFillManager.importNeurons(Map<String,TreeSet<SWCPoint>> map,
ColorRGB color,
String spatialUnit)
Import neuron(s) as a collection of reconstruction nodes (SWC points)
|
List<Tree> |
PathAndFillManager.importSWCs(Map<String,String> swcs,
ColorRGB color)
Imports a group of SWC files (Remote URLs supported).
|
static List<Tree> |
Tree.listFromDir(String dir)
Retrieves a list of
Trees from reconstruction files stored in a
common directory. |
static List<Tree> |
Tree.listFromDir(String dir,
String pattern)
Retrieves a list of
Trees from reconstruction files stored in a
common directory matching the specified criteria. |
static List<Tree> |
Tree.listFromDir(String dir,
String pattern,
String... swcTypes)
Retrieves a list of
Trees from reconstruction files stored in a
common directory matching the specified criteria. |
static Collection<Tree> |
Tree.listFromFile(String tracesOrJsonFile)
Retrieves a list of
Trees from a single file. |
| Modifier and Type | Method and Description |
|---|---|
void |
SciViewSNT.addTree(Tree tree)
Adds a tree to the associated SciView instance.
|
void |
PathAndFillManager.addTree(Tree tree)
Adds a
Tree. |
void |
Tree.applyProperties(Tree tree) |
graphics.scenery.Node |
SciViewSNT.getTreeAsSceneryNode(Tree tree)
Gets the specified Tree as a Scenery Node.
|
void |
SNTService.loadTree(Tree tree)
Loads the specified tree.
|
boolean |
Tree.merge(Tree tree)
Appends all paths of a specified
Tree to this one. |
boolean |
SciViewSNT.removeTree(Tree tree)
Removes the specified Tree.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
Tree.assignUniqueColors(Collection<Tree> trees) |
| Modifier and Type | Field and Description |
|---|---|
protected Tree |
TreeAnalyzer.tree |
| Modifier and Type | Method and Description |
|---|---|
Tree |
TreeAnalyzer.getParsedTree()
Returns the set of parsed Paths.
|
| Modifier and Type | Method and Description |
|---|---|
Collection<Tree> |
MultiTreeStatistics.getGroup()
Gets the collection of Trees being analyzed.
|
List<Tree> |
SkeletonConverter.getTrees()
Generates a list of
Trees from the skeleton image. |
List<Tree> |
MultiTreeColorMapper.sortedMappedTrees() |
| Modifier and Type | Method and Description |
|---|---|
void |
NodeStatistics.assignBranches(Tree tree)
Associates the nodes being analyzed to the branches of the specified tree
|
Map<BrainAnnotation,int[]> |
NodeStatistics.getAnnotatedFrequenciesByHemisphere(int level,
Tree tree) |
SNTChart |
NodeStatistics.getAnnotatedFrequencyHistogram(int depth,
String hemisphere,
Tree tree)
Retrieves the histogram of count frequencies across brain areas of the
specified ontology level across the specified hemisphere.
|
void |
TreeColorMapper.map(Tree tree,
LinearProfileStats stats,
ColorTable colorTable)
Colorizes a tree using Sholl data.
|
void |
TreeColorMapper.map(Tree tree,
String measurement,
ColorTable colorTable)
Colorizes a tree after the specified measurement.
|
void |
TreeColorMapper.map(Tree tree,
String measurement,
String lut)
Colorizes a tree after the specified measurement.
|
| Modifier and Type | Method and Description |
|---|---|
void |
GroupedTreeStatistics.addGroup(Collection<Tree> group,
String groupLabel)
Adds a comparison group to the analysis queue.
|
void |
GroupedTreeStatistics.addGroup(Collection<Tree> group,
String groupLabel,
String... swcTypes)
Adds a comparison group to the analysis queue.
|
static TreeStatistics |
TreeStatistics.fromCollection(Collection<Tree> trees,
String metric) |
void |
TreeColorMapper.mapTrees(List<Tree> trees,
String lut)
Colorizes a list of trees, with each tree being assigned a LUT index.
|
| Constructor and Description |
|---|
NodeStatistics(Collection<T> points,
Tree tree)
Performs statistics on a collection of nodes.
|
PathProfiler(Tree tree,
Dataset dataset) |
PathProfiler(Tree tree,
ij.ImagePlus imp)
Instantiates a new Profiler
|
PersistenceAnalyzer(Tree tree) |
RoiConverter(Tree tree)
Instantiates a new Converter.
|
RoiConverter(Tree tree,
ij.ImagePlus imp)
Instantiates a new Converter.
|
ShollAnalyzer(Tree tree)
Instantiates a new Sholl analyzer using default settings, i.e., focused on
Tree's root; using sampling step size of average inter-node distance; curve
fitting enabled; and all other parameters left to defaults/auto-discovery.
|
StrahlerAnalyzer(Tree tree) |
TreeAnalyzer(Tree tree)
Instantiates a new Tree analyzer.
|
TreeStatistics(Tree tree)
Instantiates a new instance from a collection of Paths
|
| Constructor and Description |
|---|
MultiTreeColorMapper(Collection<Tree> trees)
Instantiates the MultiTreeColorMapper.
|
MultiTreeStatistics(Collection<Tree> group)
Instantiates a new instance from a collection of Trees.
|
MultiTreeStatistics(Collection<Tree> group,
String... swcTypes)
Instantiates a new instance from a collection of Trees.
|
| Modifier and Type | Method and Description |
|---|---|
static Tree |
GraphUtils.createTree(org.jgrapht.Graph<SWCPoint,?> graph)
Deprecated.
|
Tree |
DirectedWeightedSubgraph.getTree()
Returns the tree associated with the parent's graph
|
Tree |
DirectedWeightedGraph.getTree()
Returns a new tree associated with this graph, using the current state of the
graph to build the tree.
|
Tree |
DirectedWeightedGraph.getTree(boolean createNewTree)
Returns a tree associated with this graph.
|
Tree |
DirectedWeightedGraph.getTreeWithSamePathStructure()
Attempt to build a new Tree with the same
Path hierarchy as the source Tree. |
| Modifier and Type | Method and Description |
|---|---|
List<Tree> |
DirectedWeightedGraph.getTrees()
Return the connected components of this graph as a list of
Trees |
List<Tree> |
AnnotationGraph.getTrees() |
| Modifier and Type | Method and Description |
|---|---|
static DirectedWeightedGraph |
GraphUtils.createGraph(Tree tree)
Deprecated.
|
| Constructor and Description |
|---|
DirectedWeightedGraph(Tree tree)
Creates a DirectedWeightedGraph from a Tree with edge weights corresponding
to inter-node distances.
|
DirectedWeightedGraph(Tree tree,
boolean assignDistancesToWeight)
Creates a DirectedWeightedGraph from a Tree, with the option to assign edge weights corresponding
to inter-node distances.
|
| Constructor and Description |
|---|
AnnotationGraph(Collection<Tree> trees,
String metric,
double threshold,
int maxOntologyDepth) |
| Modifier and Type | Method and Description |
|---|---|
Tree |
TreeParser.getTree()
Returns the tree associated with this parser
|
| Constructor and Description |
|---|
TreeParser(Tree tree)
Instantiates a new Tree Parser.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
AllenUtils.assignHemisphereTags(Tree tree) |
static void |
AllenUtils.assignToLeftHemisphere(Tree tree) |
static void |
AllenUtils.assignToRightHemisphere(Tree tree) |
static boolean |
AllenUtils.isLeftHemisphere(Tree tree)
Checks the hemisphere a neuron belongs to.
|
| Modifier and Type | Method and Description |
|---|---|
Tree |
MouseLightLoader.getTree()
Script-friendly method to extract the entire neuron as a collection of Paths.
|
Tree |
InsectBrainLoader.getTree()
Gets the collection of Paths for the specified cell ID
|
Tree |
RemoteSWCLoader.getTree(String cellId) |
Tree |
NeuroMorphoLoader.getTree(String cellId)
Gets the collection of Paths for the specified cell ID
|
Tree |
MouseLightLoader.getTree(String compartment)
Script-friendly method to extract a compartment as a collection of Paths.
|
Tree |
FlyCircuitLoader.getTree(String cellId)
Gets the collection of Paths for the specified cell ID
|
Tree |
MouseLightLoader.getTree(String compartment,
ColorRGB color)
Extracts a cell compartment as a collection of Paths.
|
| Modifier and Type | Method and Description |
|---|---|
static Map<String,Tree> |
MouseLightLoader.extractTrees(File jsonFile,
String compartment)
Extracts reconstruction(s) from a JSON file.
|
static Map<String,Tree> |
MouseLightLoader.extractTrees(InputStream stream,
String compartment) |
| Constructor and Description |
|---|
PathOrderAnalysisCmd(Tree tree) |
StrahlerCmd(Tree tree)
Instantiates a new StrahlerCmd.
|
| Modifier and Type | Method and Description |
|---|---|
Tree |
Viewer3D.getTree(String label)
Gets the tree associated with the specified label.
|
| Modifier and Type | Method and Description |
|---|---|
List<Tree> |
Viewer3D.getTrees()
Returns all trees added to this viewer.
|
List<Tree> |
Viewer3D.getTrees(boolean visibleOnly)
Returns all trees added to this viewer.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Viewer2D.add(Tree tree)
Appends a tree to the viewer using default options.
|
void |
Viewer2D.add(Tree tree,
ColorRGB color)
Appends a tree to the viewer.
|
void |
Viewer2D.add(Tree tree,
String color)
Appends a tree to the viewer.
|
void |
Viewer2D.add(Tree tree,
String measurement,
ColorTable colorTable,
double min,
double max)
Appends a tree to the viewer rendered after the specified measurement.
|
void |
Viewer2D.add(Tree tree,
String measurement,
String lut)
Appends a tree to the viewer rendered after the specified measurement.
|
void |
Viewer2D.add(Tree tree,
String measurement,
String lut,
double min,
double max)
Appends a tree to the viewer rendered after the specified measurement.
|
void |
Viewer3D.addTree(Tree tree)
Adds a tree to this viewer.
|
void |
Viewer2D.addTree(Tree tree)
Deprecated.
Use
Viewer2D.add(Tree) instead |
boolean |
Viewer3D.removeTree(Tree tree)
Removes the specified Tree.
|
void |
Viewer3D.translate(Tree tree,
SNTPoint offset)
Translates the specified Tree.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Viewer2D.add(List<Tree> trees,
String lut)
Adds a list of trees while assigning each tree to a LUT index.
|
void |
Viewer3D.addTrees(Collection<Tree> trees,
boolean assignUniqueColors)
Deprecated.
use
Viewer3D.addTrees(Collection, String) instead |
void |
Viewer3D.addTrees(Collection<Tree> trees,
String color)
Adds a collection of trees.
|
void |
Viewer3D.addTrees(Collection<Tree> trees,
String color,
double transparencyPercent)
Adds a collection of trees.
|
void |
Viewer3D.addTrees(Collection<Tree> trees,
String color,
String... commonTags)
Adds a collection of trees.
|
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