Package sc.fiji.snt.analysis.sholl.parsers

Class ImageParser2D

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.sholl.parsers.ImageParser

sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

All Implemented Interfaces:

Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.plugin.SciJavaPlugin, Parser, ProfileProperties

public class ImageParser2D
extends ImageParser

Sholl Parser for 2D images

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field	Description
final int	MAX_N_SPANS
static final int	MEAN	Flag for integration of repeated measures: average
static final int	MEDIAN	Flag for integration of repeated measures: median
static final int	MODE	Flag for integration of repeated measures: mode

Fields inherited from class sc.fiji.snt.analysis.sholl.parsers.ImageParser

cal, center, channel, frame, imp, lowerT, maxX, maxY, maxZ, minX, minY, minZ, profile, properties, radii, running, start, statusService, upperT, voxelSize, xc, yc, zc

Fields inherited from interface sc.fiji.snt.analysis.sholl.ProfileProperties

HEMI_EAST, HEMI_NONE, HEMI_NORTH, HEMI_SOUTH, HEMI_WEST, INTG_MEAN, INTG_MEDIAN, INTG_MODE, KEY_2D3D, KEY_CALIBRATION, KEY_CENTER, KEY_CHANNEL_POS, KEY_EFFECTIVE_STEP_SIZE, KEY_EXTRA_MEASUREMENT, KEY_FRAME_POS, KEY_HEMISHELLS, KEY_ID, KEY_NSAMPLES, KEY_NSAMPLES_INTG, KEY_SLICE_POS, KEY_SOURCE, KEY_THRESHOLD_RANGE, SRC_IMG, SRC_TABLE, SRC_TRACES, UNSET

Constructor Summary

Constructors

Constructor	Description
ImageParser2D(ij.ImagePlus imp)
ImageParser2D(ij.ImagePlus imp, org.scijava.Context context)

Method Summary

Modifier and Type	Method	Description
Profile	getProfile()	Gets the Sholl profile generated by the parsing operation.
void	parse()	Performs the parsing operation to extract the Sholl profile.
void	setAggressiveSpikeSuppression(boolean enabled)	Sets experimental spike suppression mode.
void	setCenter(double x, double y)
void	setCenterPx(int x, int y)
void	setPosition(int channel, int slice, int frame)
void	setRadii(double startRadius, double step, double endRadius)
void	setRadii(double startRadius, double step, double endRadius, int span, int integrationFlag)
void	setRadiiSpan(int nSamples, int integrationFlag)

Methods inherited from class sc.fiji.snt.analysis.sholl.parsers.ImageParser

checkUnsetFields, checkUnsetFields, clearStatus, getCircumferencePoints, getIsotropicVoxelSize, getMask, getMaskProcessor, isRetrieveIntDensitiesSet, maxPossibleRadius, reset, run, setCenter, setCenterFromROI, setCenterFromROI, setCenterPx, setHemiShells, setPosition, setRadii, setRetrieveIntDensities, setThreshold, successful, terminate, withinBounds, withinThreshold, withinXYbounds, withinZbounds

Methods inherited from class org.scijava.command.ContextCommand

cancel, getCancelReason, isCanceled

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.scijava.Contextual

setContext

Field Details

MEAN

public static final int MEAN

Flag for integration of repeated measures: average

See Also:

• Constant Field Values

MEDIAN

public static final int MEDIAN

Flag for integration of repeated measures: median

See Also:

• Constant Field Values

MODE

public static final int MODE

Flag for integration of repeated measures: mode

See Also:

• Constant Field Values

MAX_N_SPANS

public final int MAX_N_SPANS

See Also:

• Constant Field Values

Constructor Details

ImageParser2D

public ImageParser2D(ij.ImagePlus imp)

ImageParser2D

public ImageParser2D(ij.ImagePlus imp,
 org.scijava.Context context)

Method Details

setCenterPx

public void setCenterPx(int x,
 int y)

setCenter

public void setCenter(double x,
 double y)

setAggressiveSpikeSuppression

public void setAggressiveSpikeSuppression(boolean enabled)

Sets experimental spike suppression mode.

When sampling binarized images, jagged (ladder-like) foreground edges can produce single-pixel "spikes" that go tangent to the sampling shell, registering as spurious intersections. This is not an algorithmic problem with Sholl analysis itself: it is an inherent consequence of rasterized circles intersecting rasterized structures.

By default, (off), SNT uses legacy stair-aware suppression that only removes isolated ring hits matching specific diagonal staircase patterns in the source image. This is the same behavior as v4.x and is safe for all image types including skeletonized (1-pixel wide) structures.

When enabled, SNT applies a stricter 1D morphological opening on the ring: any foreground pixel whose immediate ring neighbors are both background is suppressed. This effectively removes single-pixel noise but will also suppress genuine intersections where a thin neurite crosses the sampling shell at a steep angle, producing exactly one foreground pixel on the ring. Do not use with skeletonized images.

Parameters:

enabled - if true, applies aggressive 1D ring suppression (suitable for thick processes only). If false (default), uses legacy stair-aware suppression compatible with all image types.

setRadii

public void setRadii(double startRadius,
 double step,
 double endRadius)

Overrides:

setRadii in class ImageParser

setRadii

public void setRadii(double startRadius,
 double step,
 double endRadius,
 int span,
 int integrationFlag)

setRadiiSpan

public void setRadiiSpan(int nSamples,
 int integrationFlag)

getProfile

public Profile getProfile()

Description copied from interface: Parser

Gets the Sholl profile generated by the parsing operation.

This method returns the profile containing intersection counts at various radial distances. The profile should only be retrieved after calling Parser.parse() and verifying success with Parser.successful().

Specified by:

getProfile in interface Parser

Overrides:

getProfile in class ImageParser

Returns:

the Sholl profile, or null if parsing has not been performed or was unsuccessful

parse

public void parse()

Description copied from interface: Parser

Performs the parsing operation to extract the Sholl profile.

This method analyzes the data source and computes intersection counts at various radial distances from the center point. The resulting profile can be retrieved using Parser.getProfile().

Implementations should handle any necessary preprocessing, validation, and error handling during the parsing process.

Specified by:

parse in interface Parser

Overrides:

parse in class ImageParser

setPosition

public void setPosition(int channel,
 int slice,
 int frame)