| Package | Description |
|---|---|
| sc.fiji.snt.analysis.sholl |
Sholl analysis of Images, pre-sampled data and
Trees. |
| sc.fiji.snt.analysis.sholl.gui |
GUI customizations (image overlays, plots, etc.) required for Sholl Analysis.
|
| sc.fiji.snt.analysis.sholl.math |
Statistical analysis of Sholl data
|
| sc.fiji.snt.analysis.sholl.parsers |
Parsers to retrieve Profiles from multiple sources (2D/3D images, reconstructions, and tables)
|
| sc.fiji.snt.util |
Miscellaneous SNT utilities, including classes defining reconstruction nodes.
|
| Modifier and Type | Field and Description |
|---|---|
Set<ShollPoint> |
ProfileEntry.points
List of intersection points associated with the entry's radius (in
spatially calibrated units)
|
| Modifier and Type | Method and Description |
|---|---|
ShollPoint |
Profile.center() |
| Modifier and Type | Method and Description |
|---|---|
ArrayList<Set<ShollPoint>> |
Profile.points() |
| Modifier and Type | Method and Description |
|---|---|
void |
ProfileEntry.addPoint(ShollPoint point) |
void |
ProfileEntry.removePoint(ShollPoint point) |
void |
Profile.setCenter(ShollPoint center) |
| Modifier and Type | Method and Description |
|---|---|
void |
ProfileEntry.assignPoints(Set<ShollPoint> points) |
| Constructor and Description |
|---|
ProfileEntry(Number r,
Number count,
Set<ShollPoint> points) |
ProfileEntry(Number r,
Set<ShollPoint> points) |
| Modifier and Type | Method and Description |
|---|---|
void |
ShollPlot.markPoint(ShollPoint point,
Color color)
Highlights a point on a plot using the default marker.
|
void |
ShollPlot.markPoint(ShollPoint pCentroid,
int markShape,
int markSize)
Highlights a point on a plot without listing it on the Plot's table.
|
| Modifier and Type | Method and Description |
|---|---|
ShollPoint |
LinearProfileStats.getCenteredMaximum() |
ShollPoint |
LinearProfileStats.getCenteredMaximum(boolean fittedData)
Returns the average coordinates of all maxima.
|
ShollPoint |
LinearProfileStats.getCentroid() |
ShollPoint |
LinearProfileStats.getCentroid(boolean fittedData)
Retrieves the centroid from all pairs of data (radius, inters.
|
ShollPoint |
LinearProfileStats.getPolygonCentroid() |
ShollPoint |
LinearProfileStats.getPolygonCentroid(boolean fittedData)
Calculates the centroid from all (radius, inters.
|
| Modifier and Type | Method and Description |
|---|---|
ArrayList<ShollPoint> |
LinearProfileStats.getMaxima() |
ArrayList<ShollPoint> |
LinearProfileStats.getMaxima(boolean fittedData)
Returns a list of all the points in the linear Sholl profile associated
with the highest intersections count
|
Set<ShollPoint> |
LinearProfileStats.getPolynomialMaxima(double lowerBound,
double upperBound,
double initialGuess)
Calculates local maxima (critical points at which the derivative of the
polynomial is zero) within the specified interval.
|
| Modifier and Type | Field and Description |
|---|---|
protected ShollPoint |
ImageParser.center |
| Modifier and Type | Method and Description |
|---|---|
protected HashSet<ShollPoint> |
ImageParser3D.getUnique3Dgroups(ArrayList<ShollPoint> points) |
protected Set<ShollPoint> |
ImageParser2D.groupPositions(int[][] points) |
protected Set<ShollPoint> |
ImageParser2D.targetGroupsPositions(int[] pixels,
int[][] rawpoints) |
| Modifier and Type | Method and Description |
|---|---|
protected HashSet<ShollPoint> |
ImageParser3D.getUnique3Dgroups(ArrayList<ShollPoint> points) |
| Modifier and Type | Method and Description |
|---|---|
static ShollPoint |
ShollPoint.fromString(String string) |
| Modifier and Type | Method and Description |
|---|---|
static void |
ShollPoint.scale(Set<ShollPoint> set,
ij.measure.Calibration cal) |
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