Module org.scijava.ops.image

Package org.scijava.ops.image.coloc.saca

Class SACAHeatmapZScore<I extends RealType<I>>

java.lang.Object

org.scijava.ops.image.coloc.saca.SACAHeatmapZScore<I>

Type Parameters:

I - input type

All Implemented Interfaces:

Computers.Arity5<RandomAccessibleInterval<I>,RandomAccessibleInterval<I>,I,I,Long,RandomAccessibleInterval<DoubleType>>, Consumers.Arity6<RandomAccessibleInterval<I>,RandomAccessibleInterval<I>,I,I,Long,RandomAccessibleInterval<DoubleType>>

public class SACAHeatmapZScore<I extends RealType<I>>
extends Object
implements Computers.Arity5<RandomAccessibleInterval<I>,RandomAccessibleInterval<I>,I,I,Long,RandomAccessibleInterval<DoubleType>>

Author:

Shulei Wang, Curtis Rueden, Ellen TA Dobson, Edward Evans

Implementation Note:

op names='coloc.saca.heatmapZScore', priority='100.'

Constructor Summary

Constructors

Constructor	Description
SACAHeatmapZScore()

Method Summary

Modifier and Type	Method	Description
void	compute(RandomAccessibleInterval<I> image1, RandomAccessibleInterval<I> image2, I thres1, I thres2, Long seed, RandomAccessibleInterval<DoubleType> result)	Spatially Adaptive Colocalization Analysis (SACA) Z-score heatmap.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.function.Computers.Arity5

accept

Methods inherited from interface org.scijava.function.Consumers.Arity6

andThen

Constructor Detail

SACAHeatmapZScore

public SACAHeatmapZScore()

Method Detail

compute

public void compute(RandomAccessibleInterval<I> image1,
                    RandomAccessibleInterval<I> image2,
                    I thres1,
                    I thres2,
                    Long seed,
                    RandomAccessibleInterval<DoubleType> result)

Spatially Adaptive Colocalization Analysis (SACA) Z-score heatmap. This Op utilizes the SACA framework to identify colocalized pixels and their strength as a Z-score heatmap. The Z-score heatmap is a produced by Shulei's adaptive smoothed kendall tau algorithim. SACA was adapted from Shulei's java code for AdaptiveSmoothedKendallTau in his RKColocal package (https://github.com/lakerwsl/RKColocal/blob/master/RKColocal_0.0.1.0000.tar.gz).

Specified by:

compute in interface Computers.Arity5<RandomAccessibleInterval<I extends RealType<I>>,RandomAccessibleInterval<I extends RealType<I>>,I extends RealType<I>,I extends RealType<I>,Long,RandomAccessibleInterval<DoubleType>>

Parameters:

image1 - input image 1

image2 - input image 2

thres1 - threshold 1 value; otsu threshold applied if null

thres2 - threshold 2 value; otsu threshold applied if null

seed - seed value to use; default 0xdeadbeefL

result - Adaptive smoothed kendall tau Z-score heatmap (i.e. colocalization strength)