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Microscopy Image Browser
1.233
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Calculate correlation coefficients for img, script to run from Correlation panel of im_browser. More...
Functions | |
function [
corr_coef , model , objMask , smooth_corr , granularity , roi_size ] = | calc_correlation (img, img_mask, mode, type, slope_length, darkthres, dt, auto_thres, inv_sw, a_contrast, relative_to_frame, objMask) |
Calculate correlation coefficients for img, script to run from Correlation panel of im_browser. More... | |
Calculate correlation coefficients for img, script to run from Correlation panel of im_browser.
function [ corr_coef , model , objMask , smooth_corr , granularity , roi_size ] = calc_correlation | ( | img, | |
img_mask, | |||
mode, | |||
type, | |||
slope_length, | |||
darkthres, | |||
dt, | |||
auto_thres, | |||
inv_sw, | |||
a_contrast, | |||
relative_to_frame, | |||
objMask | |||
) |
Calculate correlation coefficients for img, script to run from Correlation panel of im_browser.
img | - stack of images (h,w,color_channel,frame) |
img_mask | - take only part of the original image into analysis. Mask(h,w) defines the area for analysis |
mode | - mode, Absolute, Relative (current-previous), Relative cummulative |
type | - type of correlation: Pearson, Overlap, Manders, Intersection... |
slope_length | - number of frames to be used for smoothing calculation |
darkthres | - object separation threshold, use 0 to analyse the whole image |
dt | - time between frames |
auto_thres | - [optional] automatic thresholding by Otsu's method switch: 0 - off, 1 - on |
inv_sw | - [optional] instead of correlation, return displacement, usually 1-minus-correlation |
a_contrast | - [optional] if not NaN, is used for adjust contrast individually for each roi box in each frame |
relative_to_frame | - [optional] frame number for absolute mode |
objMask | - [optional] provide object mask for analysis |
corr_coef | - vector with amplitudes of correlation coefficients |
model | - difference map, current_frame -minus- previous |
objMask | - object mask, generated with Otsu's method or with specified threshold value (darkthres) |
smooth_corr | - smoothed correlation coefficient with the window size=slope_length |
granularity | - granularity of the objMask |
roi_size | - size of the roi object in pixels |
Types of coefficients:
Referenced by ib_calcCorrelation().