applyctf#

summary#

Apply one of three CTF correction methods to a stack of images.

  1. Apply a simple phase flip that leaves the amplitudes unmodulated.

  2. Apply the CTF via multiplication, which damps noise near the CTF zeros.

  3. Apply a low-resolution boosting Wiener filter that produces images with contrast similar to a phase plate image. Based of the filter suggested by Dimitry Tegunove [link to repo] and also as implemented in emClarity as the “phakePhasePlate” option. [link to repo]

Note

The Wiener filter is only available in the newer alpha versions.

cli options#

none

interactive options#

input_filename

  • The input file, containing one or more images in a stack.

output_filename

  • The output file.

pixel_size

  • Pixel size of input images in Angstroms.

acceleration_voltage

  • Acceleration voltage, in keV.

spherical_aberration

  • Objective lens spherical aberration in mm.

amplitude_contrast

  • Fraction of total contrast attributed to amplitude contrast.

input_ctf_values_from_text_file

  • Use a text file to input defocus values? If yes, a text file with one line per image is required

phase_flip_only

  • Phase Flip Only. If Yes, only phase flipping is performed.

apply_wiener_filter

Apply Wiener Filter. If Yes, apply Wiener filter as suggested by Dimitry Tegunov.

maintain_image_contrast

  • Maintain image contrast. If Yes, contrast is the same as image.