java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmFRETEfficiency

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmFRETEfficiency
extends AlgorithmBase
```
Fluorescence Resonance Energy Transfer FRET refers to the nonradiative transfer of energy from an excited state donor fluorescent molecule to a nearby acceptor fluorescent molecule. The energy transfer efficiency E, defined as the number of energy transfer events divided by the number of photons absorbed by the donor, is related to the distance R between the acceptor and donor by: E = 1/[1 + (r/R0)**6] (eq. 1) where R0, the Forster critical distance, is the distance at which E = 0.5. We also have E = 1 - FDA/FD, (eq. 2) where FDA is the donor fluorescence in the presence of an acceptor and FD is the donor fluorescence in the absence of the acceptor. The equivalent of an acceptor's absence can be created by photobleaching the acceptor. Thus, a method using equation 2, can be performed on a single sample by measuring the donor fluorescence before and after photobleaching the acceptor molecules.
Because FRET falls off as the sixth power of the distance between the donor and the acceptor, no FRET occurs for distances greater than 2R0. Since R0 is on the order of 10 to 70 Angstroms, by performing FRET measurements it is possible to distinguish proteins that are merely nearby in the same compartment from those proteins that are interacting with each other.

The code here is a port of the MATLAB routine Two_D_Sensitized_FRET provided by Dr. Stephen Lockett.

The code here requires 3 images - image donor and acceptor dyes taken with a donor filter, image with donor and acceptor dyes taken with a FRET filter, and image with donor and acceptor dyes taken with an acceptor filter. Only 1 color will be used from a color image.

The code here requires the user to provide 4 bleed thru parameters. AlgorithmFRETBleedThrough will be used to obtain the 4 bleed thru parameters. The DFP into FRET bleed thru and the DFP into AFP bleed thru will be obtained from 1 run of AlgorithmFRETBleedThrough on a set of 3 images containing donor dye only. The AFP into FRET bleed thru and the AFP into DFP bleed thru will be obtained from 1 run of AlgorithmFRETBleedThrough on a set of 3 images containing acceptor dye only. Then AlgorithmFRETEfficiency is run with a set of 3 images containing both donor and acceptor dye, so obtaining the FRET efficiency requires a set of 9 images.

The code here assumes the presence of 2 or more VOI regions - a backgorund region and 1 or more active regions whose areas are used for the efficiency calculations. Pixels with saturation values in any of the 3 images are excluded from all calculations. The VOIs must all be placed in the source image and the source image must be the image with donor and acceptor dyes taken with a donor fluorescent peak filter. Radio buttons in the dialog box are used to select an active VOI or a blue background VOI. Either an ellipse VOI, rectangle VOI, levelset VOI, or polyline VOI will be selected from the top MIPAV toolbar. Hit the NEW_VOI button to create other active VOIs. Just do not use blue as an active VOI color. The background region will have a smaller average intensity than the active region.

This program outputs the FRET efficiency and the adjusted donor and adjusted acceptor intensities for each active VOI region. Optionally, the user may create floating point images with the adjustedFRET/adjusted donor, adjustedFRET/adjusted acceptor or efficiency given at every pixel location.

Reference: 1.) "Imaging Protein-Protein Interactions Using Fluorescence Energy Transfer Microscopy" by Anne K. Kenworthy, Methods, 24, 2001, pp. 289 - 296.

2.) "Quantitative Fluorescence Resonance Energy Transfer Measurements Using Fluorescence Microscopy" by Gerald W. Gordon, Gail Berry, Xiao Huan Liang, Beth Levine, and Brian Herman, Biophysical Journal, Volume 74, May, 1998, pp. 2702-2713.

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private ModelImage`	`acceptorImage`	DOCUMENT ME!
`private float`	`AFPintoDFP`	DOCUMENT ME!
`private float`	`AFPintoFRET`	DOCUMENT ME!
`private float`	`DFPintoAFP`	DOCUMENT ME!
`private float`	`DFPintoFRET`	DOCUMENT ME!
`private ModelImage`	`efficiencyImage`	DOCUMENT ME!
`private ModelImage`	`fDivAImage`	DOCUMENT ME!
`private ModelImage`	`fDivDImage`	DOCUMENT ME!
`private ModelImage`	`FRETImage`	private ModelImage donorImage; // image taken with donor filter.
`private ViewUserInterface`	`UI`	DOCUMENT ME!
`private boolean`	`useBlue`	DOCUMENT ME!
`private boolean`	`useGreen`	DOCUMENT ME!
`private boolean`	`useRed`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmFRETEfficiency(ModelImage donorImage, ModelImage FRETImage, ModelImage acceptorImage, boolean useRed, boolean useGreen, boolean useBlue, float DFPintoFRET, float AFPintoFRET, float DFPintoAFP, float AFPintoDFP, ModelImage fDivDImage, ModelImage fDivAImage, ModelImage efficiencyImage)`	Creates a new AlgorithmFRETEfficiency object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method Description

void finalize()
Prepares this class for destruction.

void runAlgorithm()
starts the algorithm.
- Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
  actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened
- Methods inherited from class java.lang.Thread
  activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield
- Methods inherited from class java.lang.Object
  equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

acceptorImage
```
private ModelImage acceptorImage
```
DOCUMENT ME!

AFPintoDFP
```
private float AFPintoDFP
```
DOCUMENT ME!

AFPintoFRET
```
private float AFPintoFRET
```
DOCUMENT ME!

DFPintoAFP
```
private float DFPintoAFP
```
DOCUMENT ME!

DFPintoFRET
```
private float DFPintoFRET
```
DOCUMENT ME!

efficiencyImage
```
private ModelImage efficiencyImage
```
DOCUMENT ME!

fDivAImage
```
private ModelImage fDivAImage
```
DOCUMENT ME!

fDivDImage
```
private ModelImage fDivDImage
```
DOCUMENT ME!

FRETImage
```
private ModelImage FRETImage
```
private ModelImage donorImage; // image taken with donor filter.

UI
```
private ViewUserInterface UI
```
DOCUMENT ME!

useBlue
```
private boolean useBlue
```
DOCUMENT ME!

useGreen
```
private boolean useGreen
```
DOCUMENT ME!

useRed
```
private boolean useRed
```
DOCUMENT ME!

Constructor Detail

AlgorithmFRETEfficiency

public AlgorithmFRETEfficiency(ModelImage donorImage,
                               ModelImage FRETImage,
                               ModelImage acceptorImage,
                               boolean useRed,
                               boolean useGreen,
                               boolean useBlue,
                               float DFPintoFRET,
                               float AFPintoFRET,
                               float DFPintoAFP,
                               float AFPintoDFP,
                               ModelImage fDivDImage,
                               ModelImage fDivAImage,
                               ModelImage efficiencyImage)

Creates a new AlgorithmFRETEfficiency object.

Parameters:: donorImage - image taken with donor filter; FRETImage - image taken with FRET filter; acceptorImage - image taken with acceptor filter; useRed - If true, use the red color values for the FRET; useGreen - If true, use the green color values for the FRET; useBlue - If true, use the blue color values for the FRET; DFPintoFRET - DOCUMENT ME!; AFPintoFRET - DOCUMENT ME!; DFPintoAFP - DOCUMENT ME!; AFPintoDFP - DOCUMENT ME!; fDivDImage - If not null, create adjusted FRET/adjusted donor image.; fDivAImage - If not null, create adjusted FRET/adjusted acceptor image.; efficiencyImage - If not null, create efficiency image.

Method Detail
- finalize
```
public void finalize()
```
  Prepares this class for destruction.
  
  Overrides:
  
  finalize in class AlgorithmBase
- runAlgorithm
```
public void runAlgorithm()
```
  starts the algorithm.
  
  Specified by:
  
  runAlgorithm in class AlgorithmBase

Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for destruction.
`void`	`runAlgorithm()`	starts the algorithm.

Class AlgorithmFRETEfficiency

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

acceptorImage

AFPintoDFP

AFPintoFRET

DFPintoAFP

DFPintoFRET

efficiencyImage

fDivAImage

fDivDImage

FRETImage

UI

useBlue

useGreen

useRed

Constructor Detail

AlgorithmFRETEfficiency

Method Detail

finalize

runAlgorithm