Package sc.fiji.snt.plugin

Class SomaDetectorCmd

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

sc.fiji.snt.gui.cmds.CommonDynamicCmd

sc.fiji.snt.plugin.SomaDetectorCmd

All Implemented Interfaces:

Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.module.Module, org.scijava.module.MutableModule, org.scijava.plugin.SciJavaPlugin

public class SomaDetectorCmd
extends CommonDynamicCmd

Command to automatically detect the soma (cell body) in neuronal images.

Uses a combined EDT-intensity approach to find the thickest, brightest structure in the image, which typically corresponds to the soma.

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field	Description
static final String	OUTPUT_SEEDS	Adds a SeedPoint to SeedManager's SeedOverlay instead of any ROI/path/bookmark.
static final String	SCOPE_ALL

Fields inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd

EMPTY_LABEL, HEADER_HTML, snt, sntService, statusService, ui, uiService

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor	Description
SomaDetectorCmd()

Method Summary

Modifier and Type	Method	Description
void	run()

Methods inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd

cancel, cancel, error, getConfirmationEdtSafe, getPixelPositionsOfBookmarks, getPromptWithCloseHandler, getPromptWithCloseHandler, init, isCanceled, msg, notifyExternalDataLoaded, notifyLoadingEnd, notifyLoadingStart, resetUI, resetUI, resetUI, setStatus, status, warnIfMaterializedCropActive

Methods inherited from class org.scijava.command.DynamicCommand

context, getCancelReason, getContext, getInfo, getInput, getOutput, saveInputs, setContext, setInput, setOutput, uncancel

Methods inherited from class org.scijava.module.AbstractModule

getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, unresolveInput, unresolveOutput

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.module.Module

getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, isResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, setResolved, unresolveInput, unresolveOutput

Methods inherited from interface org.scijava.module.MutableModule

addInput, addInput, addOutput, addOutput, removeInput, removeOutput

Field Details

OUTPUT_SEEDS

public static final String OUTPUT_SEEDS

Adds a SeedPoint to SeedManager's SeedOverlay instead of any ROI/path/bookmark.

See Also:

• Constant Field Values

SCOPE_ALL

public static final String SCOPE_ALL

See Also:

• Constant Field Values

Constructor Details

SomaDetectorCmd

public SomaDetectorCmd()

Method Details

run

public void run()

Specified by:

run in interface org.scijava.module.MutableModule

Specified by:

run in interface Runnable

Overrides:

run in class CommonDynamicCmd