Package gov.nih.mipav.model.algorithms

Class AlgorithmFRETEfficiency

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmFRETEfficiency

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, 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

Thread.Builder, Thread.State, 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

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, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

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 Details

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 Details

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