3-cube FRET Efficiency Estimation

Based on Zal and Gascoigne, 2004

E-FRET

Eapp

Class for estimating FRET efficiency in image time series.

WF_2x_2m instance type as input is recommended

Parameters:
  • dd_img (ndarray) –

    image time series with donor excitation-donor emission

  • da_img (ndarray) –

    image time series with donor excitation-acceptor emission

  • ad_img (ndarray) –

    image time series with acceptor excitation-donor emission

  • aa_img (ndarray) –

    image time series with acceptor excitation-acceptor emission

  • abcd_list (list[int, ...]) –

    list of crosstalk coefficients

  • G_val (float) –

    gauge ("G") parameter of imaging system
Attributes:
  • DD_img (ndarray[t, x, y]) –

    image time series with donor excitation-donor emission (e.g. 435 nm - CFP ch.)

  • DA_img (ndarray[t, x, y]) –

    image time series with donor excitation-acceptor emission (e.g. 435 nm - YFP ch.)

  • AD_img (ndarray[t, x, y]) –

    image time series with acceptor excitation-donor emission (e.g. 505 nm - CFP ch.)

  • AA_img (ndarray[t, x, y]) –

    image time series with acceptor excitation-acceptor emission (e.g. 505 nm - YFP ch.)

  • a (float) –

    acceptor bleedthrough coefficient (I_DA(A) / I_AA(A))

  • b (float) –

    acceptor bleedthrough coefficient (I_DD(A) / I_AA(A))

  • c (float) –

    donor bleedthrough coefficient (I_AA(D) / I_DD(D))

  • d (float) –

    donor bleedthrough coefficient (I_DA(D) / I_DD(D))

  • G (float) –

    gauge ("G") parameter of imaging system

  • Fc_img (ndarray[t, x, y]) –

    image time series of sensitized fluorescence

  • R_img (ndarray[t, x, y]) –

    image time series of sensitized fluorescence to donor emission ratio (F_c / I_DD)

  • Eapp_img (ndarray[t, x, y]) –

    image time series of E-FRET

  • Ecorr_img (ndarray[t, x, y]) –

    image time series of E-FRET corrected for photobleaching
Source code in src/domb/fret/e_fret/e_app.py 
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
def __init__(self, dd_img:np.ndarray, da_img:np.ndarray,
             ad_img:np.ndarray, aa_img:np.ndarray,
             abcd_list:list[int,...], G_val:float, **kwargs):
    """ Class for estimating FRET efficiency in image time series.

    __WF_2x_2m instance type as input is recommended__

    Parameters
    ----------
    dd_img: ndarray [t,x,y]
        image time series with donor excitation-donor emission
    da_img: ndarray [t,x,y]
        image time series with donor excitation-acceptor emission
    ad_img: ndarray [t,x,y]
        image time series with acceptor excitation-donor emission
    aa_img: ndarray [t,x,y]
        image time series with acceptor excitation-acceptor emission
    abcd_list: list
        list of crosstalk coefficients
    G_val: float
        gauge ("G") parameter of imaging system

    Attributes
    ----------
    DD_img: ndarray [t,x,y]
        image time series with donor excitation-donor emission
        (e.g. 435 nm - CFP ch.)
    DA_img: ndarray [t,x,y]
        image time series with donor excitation-acceptor emission
        (e.g. 435 nm - YFP ch.)
    AD_img: ndarray [t,x,y]
        image time series with acceptor excitation-donor emission
        (e.g. 505 nm - CFP ch.)
    AA_img: ndarray [t,x,y]
        image time series with acceptor excitation-acceptor emission\
        (e.g. 505 nm - YFP ch.)
    a: float
        acceptor bleedthrough coefficient (I_DA(A) / I_AA(A))
    b: float
        acceptor bleedthrough coefficient (I_DD(A) / I_AA(A))
    c: float
        donor bleedthrough coefficient (I_AA(D) / I_DD(D))
    d: float
        donor bleedthrough coefficient (I_DA(D) / I_DD(D))
    G: float
        gauge ("G") parameter of imaging system
    Fc_img: ndarray [t,x,y]
        image time series of sensitized fluorescence
    R_img: ndarray [t,x,y]
        image time series of sensitized fluorescence to donor emission ratio
        (F_c / I_DD)
    Eapp_img: ndarray [t,x,y]
        image time series of E-FRET
    Ecorr_img: ndarray [t,x,y]
        image time series of E-FRET corrected for photobleaching

    """
    self.DD_img = dd_img  # 435-CFP  DD
    self.DA_img = da_img  # 435-YFP  DA
    self.AD_img = ad_img  # 505-CFP  AD
    self.AA_img = aa_img  # 505-YFP  AA

    self.a = abcd_list[0]
    self.b = abcd_list[1]
    self.c = abcd_list[2]
    self.d = abcd_list[3]

    self.G = G_val

    self.Fc_img = self.Fc_calc(dd_img=self.DD_img,
                               da_img=self.DA_img,
                               aa_img=self.AA_img,
                               a=self.a, b=self.b, c=self.c, d=self.d)

    self.R_img, self.Eapp_img = self.E_app_calc(fc_img=self.Fc_img,
                                                dd_img=self.DD_img,
                                                G=self.G)

    self.Ecorr_img = self.E_cor_calc(e_app_img=self.Eapp_img,
                                     aa_img=self.AA_img,
                                     dd_img=self.DD_img,
                                     c=self.c,
                                     **kwargs)

Coefficients Calculation

in progress