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ib_alignstacks.m File Reference

align 2 stacks together [img shiftsXY] = ib_alignstacks(S1, S2, options, shiftsXY) OUT: img -> aligned image stacks shiftsXY -> shift coefficients IN: S1 and S2 -> two stacks, that have (height x width x color x layers) or (height x width x layers) format options -> optional options.centerX -> center of the search window options.centerY -> center of the search window options.templateWidth -> half-width of the searching window options.backgroundColor -> background color: black, white, mean, or a value options.colorCh -> color channel options.method -> method: cc - the normalized cross correlation sq - the normalized sum of squared difference xcMatlab - beta of using matlab normxcorr2 options.gradientSw = 1 or 0, use gradient image or the original intensity image options.modelSwitch -> 1-defines that dataset has 3 dimensions [H,W,Z], or when 0 - 4 dimensions [H,W,C,Z] shiftsXY -> optional, when provided the function generates aligned stack using this provided coordinates of shifts More...

Functions

function [ img ,

shiftsXY ] = 
ib_alignstacks (S1, S2, options, shiftsXY)
 align 2 stacks together [img shiftsXY] = ib_alignstacks(S1, S2, options, shiftsXY) OUT: img -> aligned image stacks shiftsXY -> shift coefficients IN: S1 and S2 -> two stacks, that have (height x width x color x layers) or (height x width x layers) format options -> optional options.centerX -> center of the search window options.centerY -> center of the search window options.templateWidth -> half-width of the searching window options.backgroundColor -> background color: black, white, mean, or a value options.colorCh -> color channel options.method -> method: cc - the normalized cross correlation sq - the normalized sum of squared difference xcMatlab - beta of using matlab normxcorr2 options.gradientSw = 1 or 0, use gradient image or the original intensity image options.modelSwitch -> 1-defines that dataset has 3 dimensions [H,W,Z], or when 0 - 4 dimensions [H,W,C,Z] shiftsXY -> optional, when provided the function generates aligned stack using this provided coordinates of shifts More...
 

Detailed Description

align 2 stacks together [img shiftsXY] = ib_alignstacks(S1, S2, options, shiftsXY) OUT: img -> aligned image stacks shiftsXY -> shift coefficients IN: S1 and S2 -> two stacks, that have (height x width x color x layers) or (height x width x layers) format options -> optional options.centerX -> center of the search window options.centerY -> center of the search window options.templateWidth -> half-width of the searching window options.backgroundColor -> background color: black, white, mean, or a value options.colorCh -> color channel options.method -> method: cc - the normalized cross correlation sq - the normalized sum of squared difference xcMatlab - beta of using matlab normxcorr2 options.gradientSw = 1 or 0, use gradient image or the original intensity image options.modelSwitch -> 1-defines that dataset has 3 dimensions [H,W,Z], or when 0 - 4 dimensions [H,W,C,Z] shiftsXY -> optional, when provided the function generates aligned stack using this provided coordinates of shifts

Function Documentation

function [ img , shiftsXY ] = ib_alignstacks (   S1,
  S2,
  options,
  shiftsXY 
)

align 2 stacks together [img shiftsXY] = ib_alignstacks(S1, S2, options, shiftsXY) OUT: img -> aligned image stacks shiftsXY -> shift coefficients IN: S1 and S2 -> two stacks, that have (height x width x color x layers) or (height x width x layers) format options -> optional options.centerX -> center of the search window options.centerY -> center of the search window options.templateWidth -> half-width of the searching window options.backgroundColor -> background color: black, white, mean, or a value options.colorCh -> color channel options.method -> method: cc - the normalized cross correlation sq - the normalized sum of squared difference xcMatlab - beta of using matlab normxcorr2 options.gradientSw = 1 or 0, use gradient image or the original intensity image options.modelSwitch -> 1-defines that dataset has 3 dimensions [H,W,Z], or when 0 - 4 dimensions [H,W,C,Z] shiftsXY -> optional, when provided the function generates aligned stack using this provided coordinates of shifts

Required fields of options:

References template_matching().

Referenced by alignDatasetsDlg>continueBtn_Callback().

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