Find_Particle_Areas (LOCI Javadocs 0-SNAPSHOT API)

java.lang.Object
- loci.apps.flow.Find_Particle_Areas

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter
```
public class Find_Particle_Areas
extends Object
implements ij.plugin.filter.PlugInFilter
```
ImageJ plugin to isolate cell particles in images and image stacks. Intended to be used in realtime and offline analysis of flow cytometry experiments.
Three main functions: determining sum pixel area of cell or particle in brightfield images, determining sum pixel intensity count in intensity images, and calculating ratio of particle intensity per particle area.

Author:

Ajeetesh Vivekanandan

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static interface Find_Particle_Areas.MPFC_Ctrl

Nested Classes
Modifier and Type	Class and Description
`static interface`	`Find_Particle_Areas.MPFC_Ctrl`

Field Summary
- Fields inherited from interface ij.plugin.filter.PlugInFilter
  CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, NO_UNDO_RESET, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors
Constructor and Description
`Find_Particle_Areas()`
`Find_Particle_Areas(ij.ImagePlus image, ij.ImagePlus brightfieldImage, ij.ImagePlus intensityImage, String method, double minThresh, double sigma, int minSize, boolean excludeEdge, boolean ratioMode)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addImageToStack(ij.ImagePlus mainImage, ij.process.ImageProcessor imageToAdd, ij.ImageStack correspondingStack)`
`float[]`	`analyzeIndividualParticles()`
`void`	`analyzeSingleStack()`
`ij.ImagePlus[]`	`createRatioMask()` Creates a ratio mask stack for both brightfield and intensity images.
`ij.ImagePlus`	`findParticles(ij.ImagePlus imageToAnalyze, boolean intensityImage, boolean showResults)`
`static void`	`main(String[] args)`
`void`	`run(ij.process.ImageProcessor arg0)`
`void`	`setFullStackOption(boolean option)`
`int`	`setup(String arg, ij.ImagePlus image)` Original setup method called by ImageJ when plugin is run.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Find_Particle_Areas
```
public Find_Particle_Areas()
```

Find_Particle_Areas

public Find_Particle_Areas(ij.ImagePlus image,
                           ij.ImagePlus brightfieldImage,
                           ij.ImagePlus intensityImage,
                           String method,
                           double minThresh,
                           double sigma,
                           int minSize,
                           boolean excludeEdge,
                           boolean ratioMode)

Method Detail

setFullStackOption

public void setFullStackOption(boolean option)

main

public static void main(String[] args)

setup
```
public int setup(String arg,
                 ij.ImagePlus image)
```
Original setup method called by ImageJ when plugin is run.

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

Parameters:

arg - String arg0

image - ImagePlus image to run calculation on

run
```
public void run(ij.process.ImageProcessor arg0)
```
Specified by:

run in interface ij.plugin.filter.PlugInFilter

createRatioMask
```
public ij.ImagePlus[] createRatioMask()
```
Creates a ratio mask stack for both brightfield and intensity images. Intensity image masks contain only the pixels above threshold INSIDE the brightfield image's cell outline (if there is a cell).

Returns:

ImagePlus[] array of 2 ImagePlus objects, array[0] = brightfield Image, array[1] = intensity Image

findParticles

public ij.ImagePlus findParticles(ij.ImagePlus imageToAnalyze,
                                  boolean intensityImage,
                                  boolean showResults)

addImageToStack

public void addImageToStack(ij.ImagePlus mainImage,
                            ij.process.ImageProcessor imageToAdd,
                            ij.ImageStack correspondingStack)

analyzeSingleStack
```
public void analyzeSingleStack()
```

analyzeIndividualParticles

public float[] analyzeIndividualParticles()

Class Find_Particle_Areas

Nested Class Summary

Field Summary

Fields inherited from interface ij.plugin.filter.PlugInFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Find_Particle_Areas

Find_Particle_Areas

Method Detail

setFullStackOption

main

setup

run

createRatioMask

findParticles

addImageToStack

analyzeSingleStack

analyzeIndividualParticles