## Estimate Defocus / Astigmatism | ||||||
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Operation | Purpose | Description | Example | Input | Outputs | Subroutines |

'CTF FIND' | Estimate defocus and astigmatism from micrograph | Estimates defocus, astigmatism, and astigmatism angle for CTF starting from a micrograph. This operation is normally used on a large original micrograph since it can average multiple 2-D power spectra windowed from the micrograph. Uses CTFFIND3 developed by Nikolaus Grigorieff (licensed under the terms of the GNU Public License version 3, GPLv3). Here CTFFIND3 has been modified to output a SPIDER format power spectrum, and to output defocus and astigmatism using SPIDER conventions to operation line registers and to a line in a doc file. | Usage, ctffind.spi, ctffind.spi | Microsopy parameters & Micrograph image | Defocus and astigmatism to SPIDER registers, Defocus doc file, & Average power spectrum image | ctffind3 |

'TF DDF' | Estimate defocus and amplitude contrast | Estimates defocus, and amplitude contrast ratio (ACR) for CTF from minima in power spectrum starting with a rotationally averaged 1D power spectrum. Input can be single spectrum or a series of spectra. Outputs defocus parameters to operation line registers and to a line in a doc file. | -- | Microsopy parameters & Rotationally averaged power spectrum image(s) | Filter doc file | defocus, defo001, defo003 |

'TF CRF' | Estimate defocus & amplitude contrast | Estimates defocus, and amplitude contrast ratio (ACR)for CTF based on a cross-resolution curve between a single defocus group volume and a partial CTF-corrected volume. Outputs defocus parameters to operation line registers. | -- | Microsopy parameters & Cross Resolution doc file e.g. output of 'RF 3' | Defocus and ACR to operation line registers | tfcrf |

'CTF ED' | Estimate defocus from micrograph | Legacy operation replaced by 'CTF FIND' due to poor results. | -- | -- | -- | -- |

'TF ED' | Estimate defocus from image power spectrum | Legacy operation replaced by 'CTF FIND' due to poor results. | -- | -- | -- | -- |

## Generate CTF from Defocus & Parameters | ||||||

'TF CT' (for images) 'TF CT3' (for volumes) |
Generate a complex, phase flipping, binary, CTF image/volume | Generate the phase CTF for bright-field electron microscopy. Produces a binary or two-valued (-1,1) transfer function in complex image/volume which can be used for phase flipping. The output CTF function can be used to correct the phase of bright-field weak phase contrast image/volume using the 'TF COR' or 'TF CTS' operations. | Usage | Micrograph parameters | Complex image/volume | trafc, traftc3, tfd |

'TF C' (for images) 'TF C3' (for volumes) |
Generate complex, straight, CTF image | Generate the phase CTF for bright-field electron microscopy. Produces a straight transfer function in a complex image/volume. This CTF function can be applied, using the 'MU' or 'TF CTS' operations, to the Fourier transform of an object for correcting of the phase of bright-field weak phase contrast. | Usage. | Micrograph parameters | Complex image/volume | trafc, trafc3, trafd |

'TF LIS' (Replaces 'TF L') |
Generate CTF functions, in doc file | Generate the phase contrast transfer function for for bright-field electron microscopy. Produces listing of radii, straight transfer function, phase fipping transfer function, trapped straight transfer function, etc. in text form in a doc file. | Usage | Micrograph parameters | CTF doc file | tfd, trafl, get_tf_input |

'TF' | Generate image showing effect of defocus on CTF | Generate the phase CTF for bright-field electron microscopy for specified defoci. Produces the straight transfer function (or its square, the envelope function) within a specified defocus range and using specified electron optical parameters. Output is in the form of a SPIDER image file. | Usage | Micrograph parameters | Image | traf, tf |

'TF D' | Generate image showing effect of astigmatism on CTF | Generate the phase CTF for bright-field electron microscopy. Produces the straight transfer function (or its square, the envelope function) for a specified defocus and astigmatism using specified electron optical parameters. Output is in the form of a SPIDER image file. | Usage | Micrograph parameters | Image | tfd, trafd, trafc, trafc3 |

## CTF Correct image/volume | ||||||

'TF COR' | CTF correction, image/volume | CTF corrects an image/volume by Wiener filtering. Multiplies the FFT of the input image/volume by the CTF Fourier image. Then reverse FFT transforms this to create output image/volume. Similar to operation: 'TF CTS' without SNR adjustment. | Usage, refproj.spi | Image/volume & Complex CTF image/volume | Image/volume | rctfone |

'TF CTS' | CTF correction, with SNR, image/volume | CTF corrects a series of images/volumes by Wiener filtering. Accumulates a CTF corrected sum over all input images/volumes. Similar to 'TF COR', but divides summed input images/volumes by the summed squared CTF images/volumes and adjusts for SNR. | Usage recon.spi | Image(s)/volume(s), & Complex CTF image(s)/volume(s) | Image(s) / volume (s) | rctfss |

'TF SNR | CTF correction, with frequency dependent SNR | CTF corrects a volume series by Wiener filtering using frequency dependent SNR. Rarely used, may be buggy | -- | Image(s)/volume(s), Complex image(s)/volume(s), & SNR doc file | Image(s) / volume(s) | tfsnr |

## Other CTF related operations | ||||||

'TF LM4' | Determine CTF envelope B-factor and noise parameters | Apply nonlinear regression to estimate EM image CTF envelope B-factor and noise parameters. Outputs to operation line registers and doc file. Operation rarely used. | Usage | Rotationally averaged power spectrum image | B-factors of envelope function and CTF to operation line registers and doc file | tflm4 |

'TF DNS' | Delete noise background | Calculate the noise background from rotationally
averaged 1-D power spectrum and correct it.
The background is assumed to be a Gaussian profile:
a1 * exp[-(k/a2)**2] + a3 .
The output file is used by
'TF DEV'
for envelope function fitting. |
Usage, tfdns.spi | Rotationally averaged power spectrum image | Background corrected rotationally averaged power spectrum image | noise, defo003 |

'TF DEV' | Determine envelope function | Use a least-squares method to determine the parameters of envelope functions of the CTF from rotationally averaged power spectra images. | -- | Background corrected rotationally averaged power spectrum image | 1D image(s) | envelope |

'TF SIM' | Simulate an electron microscope image | Simulate a bright field electron microscope image of a structure by using complex atomic scattering amplitudes. Atomic information of the structure must be provided in the form of a PDB file. | -- | PDB file | Image | trafsim |

Source: ctfops.html Last update: 29 June 2016 ArDean Leith

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