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ib_alignstack.m File Reference

alignment of images within the stack [img shiftsXY] = ib_alignstack(S1, options, shiftsXY) OUT: img -> aligned dataset shiftsXY -> vector with absolute shifts, shiftsXY(1,:) - for x and shiftsXY(2,:) - for y. The shifts are calculated vs the slice with the minimum shift, i.e. the shiftsXY are always positive IN: S1 -> stack in (format, height:width:color:thickness) options -> optional, defines a center and halfwidth of the searching window options.centerX -> center of the search window options.centerY -> center of the search window options.templateWidth -> half-width of the searching window options.colorCh -> color channel to use in multicolor images options.backgroundColor -> background color: black, white, mean, or a number 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.step, step for comparison of images, default=1 shiftsXY -> optional, a matrix of [2, size(S1,3)]. When provided the function generates aligned stack using this provided coordinates of shifts More...

Functions

function [ img ,

shiftsXY ] = 
ib_alignstack (S1, options, shiftsXY)
 alignment of images within the stack [img shiftsXY] = ib_alignstack(S1, options, shiftsXY) OUT: img -> aligned dataset shiftsXY -> vector with absolute shifts, shiftsXY(1,:) - for x and shiftsXY(2,:) - for y. The shifts are calculated vs the slice with the minimum shift, i.e. the shiftsXY are always positive IN: S1 -> stack in (format, height:width:color:thickness) options -> optional, defines a center and halfwidth of the searching window options.centerX -> center of the search window options.centerY -> center of the search window options.templateWidth -> half-width of the searching window options.colorCh -> color channel to use in multicolor images options.backgroundColor -> background color: black, white, mean, or a number 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.step, step for comparison of images, default=1 shiftsXY -> optional, a matrix of [2, size(S1,3)]. When provided the function generates aligned stack using this provided coordinates of shifts More...
 

Detailed Description

alignment of images within the stack [img shiftsXY] = ib_alignstack(S1, options, shiftsXY) OUT: img -> aligned dataset shiftsXY -> vector with absolute shifts, shiftsXY(1,:) - for x and shiftsXY(2,:) - for y. The shifts are calculated vs the slice with the minimum shift, i.e. the shiftsXY are always positive IN: S1 -> stack in (format, height:width:color:thickness) options -> optional, defines a center and halfwidth of the searching window options.centerX -> center of the search window options.centerY -> center of the search window options.templateWidth -> half-width of the searching window options.colorCh -> color channel to use in multicolor images options.backgroundColor -> background color: black, white, mean, or a number 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.step, step for comparison of images, default=1 shiftsXY -> optional, a matrix of [2, size(S1,3)]. When provided the function generates aligned stack using this provided coordinates of shifts

Function Documentation

function [ img , shiftsXY ] = ib_alignstack (   S1,
  options,
  shiftsXY 
)

alignment of images within the stack [img shiftsXY] = ib_alignstack(S1, options, shiftsXY) OUT: img -> aligned dataset shiftsXY -> vector with absolute shifts, shiftsXY(1,:) - for x and shiftsXY(2,:) - for y. The shifts are calculated vs the slice with the minimum shift, i.e. the shiftsXY are always positive IN: S1 -> stack in (format, height:width:color:thickness) options -> optional, defines a center and halfwidth of the searching window options.centerX -> center of the search window options.centerY -> center of the search window options.templateWidth -> half-width of the searching window options.colorCh -> color channel to use in multicolor images options.backgroundColor -> background color: black, white, mean, or a number 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.step, step for comparison of images, default=1 shiftsXY -> optional, a matrix of [2, size(S1,3)]. 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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