CTF ED - Contrast Transfer Function - Estimate Defocus from micrograph

PURPOSE

Estimates the defocus, and cutoff at high frequencies for CTF based on a 2-D power spectrum. This operation is normally used on a large original micrograph since it can average multiple 2-D power spectra windowed from the micrograph. Outputs defocus parameters to SPIDER operation line registers and to a line in a doc file. Note: We recommend you use the 'CTF FIND' operation instead, especially if there is any astigmatism present, as this operation gives poor results for astigmatic images. The astigmatism calculation was unreliable and has been removed. Further info on the CTF related operations in SPIDER. This operation was never reliable and should not be used anymore. It is kept for historical reasons only. Use 'CTF FIND' instead.   Example.

SEE ALSO

CTF FIND

[Contrast Transfer Function - Estimation of CTF parameters]

USAGE

.OPERATION: CTF ED [def],[cutoff]

[The operation line can specify up to two optional register variables:

The first (called [def] in this example) receives the overall defocus without taking astigmatism into account.
The second (called [cutoff] in this example) receives the cutoff frequency in 1/A.]

.MICROGRAPH IMAGE FILE: MIC001
[Enter name of the micrograph file.]

.TILE SIZE, X & Y TILE PERCENT OVERLAP: 500, 20, 20
[Enter size (in pixels) of tile that is replicated over image to create an average power spectrum from the image and the percent overlap between adjacent tiles.]

.X & Y TILING BORDER: 500, 500
[Enter size of border around usable part of image (in pixels).]

.PIXEL SIZE [A] and SPHERICAL ABBERATION CS [MM]: 2.8, 2
[Enter pixel size in image in A and spherical aberration coefficient of the objective, usually referred to as CS, in mm.]

.ELECTRON VOLTAGE [Kev]: 200
[Enter the voltage of the electrons (in Kev).]

.AMPLITUDE CONTRAST RATIO [0-1]: 0.1
[Enter the amount of amplitude contrast (as a fraction). For ice images this may be about 0.1, for negative stain about 0.15. Default value is 0.1.]

. DEFOCUS NOISE DOC: DEF_NOISE_001
[Enter name for document file which will contain 4 register columns of noise information (NOT defocus values). This file will be overwritten if it already exists.]

.OUTPUT DEFOCUS DOCUMENT FILE: CTF_DEFOCUS
[Enter name for document file which will contain 3 register columns of defocus information. This file will be appended to if it already exists.]

.KEY/IMAGE NUMBER FOR DOCUMENT FILE: 1
[Enter key number for defocus document file.]

.AVERAGE POWER SPECTRUM FILE: AVG_POW
[Enter name for output file containing the average power spectrum from the tiles.]

NOTES

1. The defocus output document file contains following three register columns:
   a) - Key/Micrograph number.
   b) - Defocus.
   c) - Cutoff Frequency.
   

2. The noise output document file contains following four register columns:
   a) - Spatial freqency (1/A).
   b) - Estimated background noise: BACKGROUND_NOISE(f)**2.
   c) - Background-subtracted power spectrum: {CTF(f) * ENV(f) * SIGNAL(f)}**2 = PW(f) - BACKGROUND_NOISE(f)**2
   d) - Estimated ENV(f)**2
   

3. The model of the power spectrum is: PW(f) = {CTF(f) * ENV(f) * SIGNAL(f)}**2 + BACKGROUND_NOISE(f)**2

4. For details about this algorithm and cutoff frequency see: Z. Huang, P.R. Baldwin, and P. A. Penczek. Automated determination of parameters describing power spectra of micrograph images in electron microscopy. J. Struct. Biology 144,2003,79-94

5. Implemented by: Zhong Huang.

6. For calculating agstigmatism use the SPIDER operation 'CTF FIND' which outputs the angle and magnitude of astigmatism as determined by: CTFFIND3

SUBROUTINES

TFED

CALLER

UTIL1