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Microscopy Image Browser
1.10
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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
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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... | |
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 [ 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
References template_matching().
Referenced by alignDatasetsDlg>continueBtn_Callback().