Coloc_2 (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.coloc.Coloc_2<T>

Type Parameters:

T -

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class Coloc_2<T extends RealType<T> & NativeType<T>>
extends Object
implements ij.plugin.PlugIn
```
An ImageJ plugin which does pixel intensity correlation based colocalisation analysis on a pair of images, with optional Mask or ROI.

Author:

Daniel J. White, Tom Kazimiers, Johannes Schindelin

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

protected class Coloc_2.BoundingBox

protected class Coloc_2.MaskInfo

protected static class Coloc_2.RoiConfiguration

Nested Classes
Modifier and Type	Class and Description
`protected class`	`Coloc_2.BoundingBox`
`protected class`	`Coloc_2.MaskInfo`
`protected static class`	`Coloc_2.RoiConfiguration`

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`autoSavePdf`
`protected String`	`Ch1Name`
`protected String`	`Ch2Name`
`protected CostesSignificanceTest<T>`	`costesSignificance`
`protected boolean`	`displayImages`
`protected Histogram2D<T>`	`histogram2D`
`protected Img<T>`	`img1`
`protected int`	`img1Channel`
`protected Img<T>`	`img2`
`protected int`	`img2Channel`
`protected static int`	`index1`
`protected static int`	`index2`
`protected static int`	`indexMask`
`protected static int`	`indexRegr`
`protected static int`	`indexRoi`
`protected KendallTauRankCorrelation<T>`	`kendallTau`
`protected LiHistogram2D<T>`	`liHistogramCh1`
`protected LiHistogram2D<T>`	`liHistogramCh2`
`protected LiICQ<T>`	`liICQ`
`protected MandersColocalization<T>`	`mandersCorrelation`
`protected ArrayList<Coloc_2.MaskInfo>`	`masks`
`protected PearsonsCorrelation<T>`	`pearsonsCorrelation`
`protected static String`	`PREF_KEY`
`protected String[]`	`regressions`
`protected Coloc_2.RoiConfiguration`	`roiConfig`
`protected SpearmanRankCorrelation<T>`	`SpearmanRankCorrelation`

Constructor Summary

Constructors
Constructor and Description

Coloc_2()

Constructors
Constructor and Description
`Coloc_2()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`addIfValid(Algorithm<T> a, List<Algorithm<T>> list)` Adds the provided Algorithm to the list if it is not null.
`protected static int`	`clip(int val, int min, int max)` Clips a value to the specified bounds.
`void`	`colocalise(Img<T> image1, Img<T> image2, Coloc_2.BoundingBox roi, Img<T> mask)` Call this method to run a whole colocalisation configuration, all selected algorithms get run on the supplied images.
`AnalysisResults<T>`	`colocalise(Img<T> image1, Img<T> image2, Coloc_2.BoundingBox roi, Img<T> mask, List<ResultHandler<T>> extraHandlers)` Call this method to run a whole colocalisation configuration, all selected algorithms get run on the supplied images.
`protected RandomAccessibleInterval<T>`	`createMaskImage(RandomAccessibleInterval<T> image, RandomAccessibleInterval<BitType> mask, long[] offset, long[] size)` This method duplicates the given images, but respects ROIs if present.
`protected void`	`createMasksAndRois(Roi[] rois, int width, int height)` Creates appropriate data structures from the ROI information passed.
`protected void`	`createMasksFromImage(ij.ImagePlus imp)` This method checks if the given ImagePlus contains any masks or ROIs.
`protected boolean`	`createMasksFromRoiManager(int width, int height)` A method to fill the masks array with data based on the ROI manager.
`protected Coloc_2.MaskInfo`	`getBoundingBoxOfMask(Img<T> mask)` A method to get the bounding box from the data in the given image that is above zero.
`protected boolean`	`hasValidRoi(ij.ImagePlus imp)` Returns true if a custom ROI has been selected, i.e if the current ROI does not have the extent of the whole image.
`boolean`	`initializeSettings(ij.ImagePlus imp1, ij.ImagePlus imp2, int gdIndexMask, int gdIndexRegr, boolean gdAutoSavePdf, boolean gdDisplayImages, boolean gdDisplayShuffledCostes, boolean gdUseLiCh1, boolean gdUseLiCh2, boolean gdUseLiICQ, boolean gdUseSpearmanRank, boolean gdUseManders, boolean gdUseKendallTau, boolean gdUseScatterplot, boolean gdUseCostes, int gdPsf, int gdNrCostesRandomisations)` Programmatically initializes the colocalisation settings to match the given values.
`void`	`run(String arg0)`
`boolean`	`showDialog()`
`static Roi[]`	`split(Roi roi)` Splits a non overlapping composite ROI into its sub ROIs.

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

Field Detail

PREF_KEY
```
protected static final String PREF_KEY
```
See Also:

Constant Field Values

roiConfig

protected Coloc_2.RoiConfiguration roiConfig

masks

protected ArrayList<Coloc_2.MaskInfo> masks

regressions
```
protected String[] regressions
```

index1
```
protected static int index1
```

index2
```
protected static int index2
```

indexMask
```
protected static int indexMask
```

indexRoi
```
protected static int indexRoi
```

indexRegr
```
protected static int indexRegr
```

img1

protected Img<T extends RealType<T> & NativeType<T>> img1

img2

protected Img<T extends RealType<T> & NativeType<T>> img2

Ch1Name
```
protected String Ch1Name
```

Ch2Name
```
protected String Ch2Name
```

img1Channel
```
protected int img1Channel
```

img2Channel
```
protected int img2Channel
```

pearsonsCorrelation

protected PearsonsCorrelation<T extends RealType<T> & NativeType<T>> pearsonsCorrelation

liHistogramCh1

protected LiHistogram2D<T extends RealType<T> & NativeType<T>> liHistogramCh1

liHistogramCh2

protected LiHistogram2D<T extends RealType<T> & NativeType<T>> liHistogramCh2

liICQ

protected LiICQ<T extends RealType<T> & NativeType<T>> liICQ

SpearmanRankCorrelation

protected SpearmanRankCorrelation<T extends RealType<T> & NativeType<T>> SpearmanRankCorrelation

mandersCorrelation

protected MandersColocalization<T extends RealType<T> & NativeType<T>> mandersCorrelation

kendallTau

protected KendallTauRankCorrelation<T extends RealType<T> & NativeType<T>> kendallTau

histogram2D

protected Histogram2D<T extends RealType<T> & NativeType<T>> histogram2D

costesSignificance

protected CostesSignificanceTest<T extends RealType<T> & NativeType<T>> costesSignificance

displayImages
```
protected boolean displayImages
```

autoSavePdf
```
protected boolean autoSavePdf
```

Constructor Detail
- Coloc_2
```
public Coloc_2()
```

Method Detail

run
```
public void run(String arg0)
```
Specified by:

run in interface ij.plugin.PlugIn

showDialog
```
public boolean showDialog()
```

initializeSettings

public boolean initializeSettings(ij.ImagePlus imp1,
                                  ij.ImagePlus imp2,
                                  int gdIndexMask,
                                  int gdIndexRegr,
                                  boolean gdAutoSavePdf,
                                  boolean gdDisplayImages,
                                  boolean gdDisplayShuffledCostes,
                                  boolean gdUseLiCh1,
                                  boolean gdUseLiCh2,
                                  boolean gdUseLiICQ,
                                  boolean gdUseSpearmanRank,
                                  boolean gdUseManders,
                                  boolean gdUseKendallTau,
                                  boolean gdUseScatterplot,
                                  boolean gdUseCostes,
                                  int gdPsf,
                                  int gdNrCostesRandomisations)

Programmatically initializes the colocalisation settings to match the given values.

colocalise
```
public void colocalise(Img<T> image1,
                       Img<T> image2,
                       Coloc_2.BoundingBox roi,
                       Img<T> mask)
                throws MissingPreconditionException
```
Call this method to run a whole colocalisation configuration, all selected algorithms get run on the supplied images. You can specify the data further by supplying appropriate information in the mask structure.
NB: This method returns void for binary backwards compatibility with old code which might invoke it. If you want access to the AnalysisResults directly, call colocalise(Img, Img, Coloc_2.BoundingBox, Img, List) with null for extraHandlers.

Parameters:

image1 -

image2 -

roi -

mask -

Throws:

MissingPreconditionException

colocalise

public AnalysisResults<T> colocalise(Img<T> image1,
                                     Img<T> image2,
                                     Coloc_2.BoundingBox roi,
                                     Img<T> mask,
                                     List<ResultHandler<T>> extraHandlers)
                              throws MissingPreconditionException

Call this method to run a whole colocalisation configuration, all selected algorithms get run on the supplied images. You can specify the data further by supplying appropriate information in the mask structure.

Parameters:: image1 - First image.; image2 - Second image.; roi - Region of interest to which analysis is confined.; mask - Mask to which analysis is confined.; extraHandlers - additional objects to be notified of analysis results.
Returns:: Data structure housing the results.
Throws:: MissingPreconditionException

getBoundingBoxOfMask
```
protected Coloc_2.MaskInfo getBoundingBoxOfMask(Img<T> mask)
```
A method to get the bounding box from the data in the given image that is above zero. Those values are interpreted as a mask. It will return null if no mask information was found.

Parameters:

mask - The image to look for "on" values in

Returns:

a new MaskInfo object or null

addIfValid

protected void addIfValid(Algorithm<T> a,
                          List<Algorithm<T>> list)

Adds the provided Algorithm to the list if it is not null.

hasValidRoi
```
protected boolean hasValidRoi(ij.ImagePlus imp)
```
Returns true if a custom ROI has been selected, i.e if the current ROI does not have the extent of the whole image.

Returns:

true if custom ROI selected, false otherwise

clip

protected static int clip(int val,
                          int min,
                          int max)

Clips a value to the specified bounds.

createMasksFromImage
```
protected void createMasksFromImage(ij.ImagePlus imp)
```
This method checks if the given ImagePlus contains any masks or ROIs. If so, the appropriate date structures are created and filled.

createMasksFromRoiManager

protected boolean createMasksFromRoiManager(int width,
                                            int height)

A method to fill the masks array with data based on the ROI manager.

createMasksAndRois
```
protected void createMasksAndRois(Roi[] rois,
                                  int width,
                                  int height)
```
Creates appropriate data structures from the ROI information passed. If an irregular ROI is found, it will be put into a frame of its bounding box size and put into an Image<T>. In the end the members ROIs, masks and maskBBs will be filled if ROIs or masks were found. They will be null otherwise.

createMaskImage

protected RandomAccessibleInterval<T> createMaskImage(RandomAccessibleInterval<T> image,
                                                      RandomAccessibleInterval<BitType> mask,
                                                      long[] offset,
                                                      long[] size)
                                               throws MissingPreconditionException

This method duplicates the given images, but respects ROIs if present. Meaning, a sub-picture will be created when source images are ROI/MaskImages.

Throws:: MissingPreconditionException

split
```
public static Roi[] split(Roi roi)
```
Splits a non overlapping composite ROI into its sub ROIs.

Parameters:

roi - The ROI to split

Returns:

A list of one or more ROIs

Class Coloc_2<T extends RealType<T> & NativeType<T>>

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

PREF_KEY

roiConfig

masks

regressions

index1

index2

indexMask

indexRoi

indexRegr

img1

img2

Ch1Name

Ch2Name

img1Channel

img2Channel

pearsonsCorrelation

liHistogramCh1

liHistogramCh2

liICQ

SpearmanRankCorrelation

mandersCorrelation

kendallTau

histogram2D

costesSignificance

displayImages

autoSavePdf

Constructor Detail

Coloc_2

Method Detail

run

showDialog

initializeSettings

colocalise

colocalise

getBoundingBoxOfMask

addIfValid

hasValidRoi

clip

createMasksFromImage

createMasksFromRoiManager

createMasksAndRois

createMaskImage

split