ExponentialFitCorrection

Exponential fit based attenuation correction

SYNOPSIS

#include "dip_microscopy.h"

dip_Error dip_ExponentialFitCorrection ( in, out, method, percentile, fromWhere, hysteresis, varWeighted )

DATA TYPES

binary, integer, float

FUNCTION

This routine implements a simple absorption, reflection and bleaching correction based upon the assumption that the sum of these effects result in a exponential extinction of the signal as a function of depth. Only pixels that are non-zero are taken into account. Depending upon the chosen method, the mean or a percentile of all the non-zero pixels are calculated as a function of the slice number (depth). Then an exponential function is fitted through these slice-representing values. The starting point of the fit is determined by fromWhere. The first maximum is found with point[z+1] > hysteresis * point[z]. If the mean variant is chosen one can chose to apply a variance weighting to the fit.

ARGUMENTS

Data type	Name	Description
`dip_Image`	`in`	Input image
`dip_Image`	`out`	Output image
`dipf_ExpFitData`	`method`	Data statistic to fit on
`dip_float`	`percentile`	Percentile
`dipf_ExpFitStart`	`fromWhere`	From where to start the fit
`dip_float`	`hysteresis`	First maximum hysteresis
`dip_Boolean`	`varWeighted`	Fit with variance weights

The dipf_ExpFitData enumaration consists of the following flags:

Name	Description
`DIP_ATTENUATION_EXP_FIT_DATA_MEAN`	Fit on the mean values
`DIP_ATTENUATION_EXP_FIT_DATA_PERCENTILE`	Fit on the specified percentile of the data

The dipf_ExpFitStart enumaration consists of the following flags:

Name	Description
`DIP_ATTENUATION_EXP_FIT_START_FIRST_PIXEL`	Start fit on first pixel
`DIP_ATTENUATION_EXP_FIT_START_GLOBAL_MAXIMUM`	Start fit on global maximum
`DIP_ATTENUATION_EXP_FIT_START_FIRST_MAXIMUM`	Start fit on first maximum

LITERATURE

K.C. Strasters, H.T.M. van der Voort, J.M. Geusebroek, and A.W.M. Smeulders, "Fast attenuation correction in fluorescence confocal imaging: a recursive approach", BioImaging, vol. 2, no. 2, 1994, 78-92.

AUTHOR

Karel Strasters, adapted to DIPlib by Geert van Kempen.