TF L - Transfer Function - Send to document file

PURPOSE

Computes the phase contrast transfer function for bright-field electron microscopy. 'TF L' writes the 1-dimensional transfer function (or its square, the envelope function) in real, displayable form to a document file.

SEE ALSO

TF	[Transfer Function - Defocus dependent]
TF C	[Transfer Function - Complex]
TF C3	[Transfer Function - Complex 3D]
TF CT	[Transfer Function - phase flipping, Complex, Binary]
TF CT3	[Transfer Function - Complex, Binary 3D]
TF CTS	[Transfer Function - 2D & 3D CTF correction]
TF D	[Transfer Function - Display]
TF DDF	[Transfer Function - Determine DeFocus & amplitude contrast]
TF DEV	[Transfer Function - Determine Envelope function]
TF DNS	[Transfer Function - Determine and delete Noise background]

USAGE

.OPERATION: TF L

.CS [MM]: 2.0
[Enter the spherical aberration constant.]

.DEFOCUS[A], LAMBDA[A]: 2000,0.037
[Enter the amount of defocus, in Angstroems. Positive values correspond to underfocus (the preferred region); negative values correspond to overfocus. Next, enter the wavelength of the electrons. The value used in this example corresponds to 100kV. A table of values is listed in the glossary under lambda.]

.NUMBER OF SPATIAL FREQUENCY PTS: 128
[Enter the length of the 1D array.]

.MAXIMUM SPATIAL FREQUENCY [A-1]: 0.15
[Enter the spatial frequency radius corresponding to the maximum radius ( = 128/2 in our example) of pixels in the array. From this value, the spatial frequency increment (DK=0.15/64) is calculated.]

.SOURCE SIZE[A-1], DEFOCUS SPREAD[A]: 0.005,250
[Enter the size of the illumination source in reciprocal Angstroems. It is the size of the source as it appears in the back focal plane of the objective lens. A small value results in high coherence; a large value, low coherence. Next, enter the estimated magnitude of the defocus variations corresponding to energy spread and lens current fluctuations.]

.AMPL CONTRAST RATIO [0-1], GAUSSIAN ENV. HALFW. [FOU. UNITS]: 0.2,100
[Enter ACR and GEP; see below for definitions.]

.(D)IFFRACTOGRAM/(E)NVELOPE/(S)TRAIGHT: D
[Either the transfer function is put into the array directly as computed (option 'S'), or its square (option 'D') is stored, or else the envelope function describing the attenuation of the transfer function due to partial coherence effects (option 'E') is stored.]

.DOCUMENT FILE: TFL001
[Enter the name of the file that will store the computed function.]

NOTES

1. Theory and all definitions of electron optical parameters are according to: J. Frank (1973) Optik 38:519, and R. Wade & J. Frank (1974) Optik 49:81. Internally, the program uses the generalized coordinates defined in these papers.

2. In addition, an optional cosine term has been added with a weight, and an ad hoc Gaussian falloff function has been added as discussed in Stewart et al. (1993) EMBO J. 12:2589-2599. The complete expression is:
   TF(K) = [(1-ACR)*sin(GAMMA) - ACR*cos(GAMMA)]*ENV(K)*exp[-GEP*K^2]

SUBROUTINES

TFD, TRAFL

CALLER

UTIL1