Determine Image CTF & Tilt

Access : CP::Micrograph::Imaging Setup (Tab)

In single-particle EM data acquisition, protein specimens are often imaged by defocused beam to enhance the image contrast.  As a result, the recorded image is modulated by a Contrast Transfer Function (CTF), which can be analytically modeled and corrected during data processing.  Also, the tilting configuration of the specimen grid can be assessed by the defocus variation across the image plane.  In PARTICLE, the Micrograph::Imaging Setup module provides the functions for image CTF and tilt-geometry determination.

Image Defocus & Tilt

In a simple form, CTF can be modeled with an analytical function parameterized by a triplet: {defocus-X, defocus-Y, astigmatic angle}.  The following imaging parameters need to be defined in order to determine the CTF parameters:

• Nominal Defocus : the reading from the beam setup (for search initialization).
• Nominal Tilt : the reading from the microscope stage setup.
• Grid Geometry : FLAT or TILT conformation of the specimen plane.  In FLAT, the CTF is assumed to be constant across the image.
• Optimization : thoroughness of CTF parameter refinement.
• Pixel Size : micrograph pixel size (in Å).
• Voltage : the electron-beam accelerating voltage (in kV).
• Amplitude Contrast : the amplitude contrast in CTF (between 0.0 and 1.0).
• Spherical Aberration : spherical aberration of the optics (in mm).
• H-res : the highest resolution in CTF refinement (in Å).
• L-res : the lowest resolution in CTF refinement (in Å).
• Search Range : the search range in defocus optimization (in μm).
• Precision : the precision in defocus determination (in μm).
• Tiling Size : the dimension of tiling squares used in image power-spectrum calculation (in pixels).

After the imaging parameters have been properly defined, activate the Solve button to determine the CTF and tilt parameters of the image.  Upon completion, the result will be displayed in the designated value-boxes at the Refined Parameters group.  The Accept button will permanently enter the results to the CP::DataView spreadsheet in the project space.

Once determined, the imaging CTF and tilt parameters will be automatically incorporated into the subsequent data processing and no further action from the user is required for the CTF correction.

CTF Characteristics

In PARTICLE, CTF patterns (a.k.a. Thon Rings) can be simulated from a set of user-defined imaging parameters for experimentation.  Several display modes are available for visualizing an image power spectrum and its comparison with a theoretical CTF pattern:

•   : display a theoretical CTF pattern.
•   : display the image power spectrum.
•   : display the rotational average of the image power spectrum.
•   : compare a theoretical CTF with an image power spectrum.
•   : display peak-contours of a theoretical CTF.
•   : display the fitting zone (the highest and lowest resolution limits) for image CTF determination.