pysted.base.Fluorescence

class pysted.base.Fluorescence(lambda_, **kwargs)

This class implements a fluorescence molecule.

Parameters:

• lambda – The fluorescence wavelength (m).

• parameters – One or more parameters as described in the following table, optional.

Parameter	Default [1]	Details
sigma_ste	575: 1e-21	A dictionnary mapping STED wavelengths as integer (nm) to stimulated emission cross-section (m²).
sigma_abs	488: 3e-20	A dictionnary mapping excitation wavelengths as integer (nm) to absorption cross-section (m²).
tau	3e-9	The fluorescence lifetime (s).
tau_vib	1e-12	The vibrational relaxation (s).
tau_tri	5e-6	The triplet state lifetime (s).
qy	0.6	The quantum yield (ratio).
k0	0	Coefficient of the first first order term of the photobleaching rate
k1	1.3e-15	Coefficient of the \(b^{th}\) first order term of the photobleaching rate
b	1.4	The intersystem crossing rate (s⁻¹).
triplet_dynamics_frac	0	Fraction of the bleaching which is due to the (very long) triplets dynamics. Caution: not based on rigorous theory

[1]

EGFP (k1 and b for ATTO647N from [Oracz2017])

Fluorescence.get_k_bleach(lambda_ex, ...)	Compute a spatial map of the photobleaching rate.
Fluorescence.get_photons(intensity[, lambda_])	Translate a light intensity to a photon flux.
Fluorescence.get_psf(na, datamap_pixelsize)	Compute the Gaussian-shaped fluorescence PSF.
Fluorescence.get_sigma_abs(lambda_)	Return the absorption cross-section of the fluorescence molecule given the wavelength.
Fluorescence.get_sigma_ste(lambda_)	Return the stimulated emission cross-section of the fluorescence molecule given the wavelength.