Tomogram Set

The tomogram set describes all the tomograms (i.e. tilt series) defined in a project, and is usually named tomograms.star. It contains T+1 tables, where T is the number of tomograms.

The first table (named global) defines the properties pertaining to each tomogram. Each row corresponds to one tomogram, and it lists the following properties:

• The tomogram name (rlnTomoName): a unique identifier used to refer to this tomogram within the entire project (i.e. within the tomogram set, the particle set and the manifold set)
• The tilt series file name (rlnTomoTiltSeriesName): the path to the image stack
• The frame count (rlnTomoFrameCount)
• The tomogram size (rlnTomoSize<X/Y/Z>): the extent of the tomogram region in 3D space
• The handedness (rlnTomoHand): this value is either +1 or -1, and it describes whether the focus increases or decreases as a function of depth (projected Z coordinate). It cannot be known a priori and has to be determined experimentally. It is typically identical across the entire data set.
• The pixel size of the tilt series, given in Å
  (rlnTomoTiltSeriesPixelSize)
• The voltage, given in kV (rlnVoltage)
• The spherical aberration, given in mm^-1
  (rlnSphericalAberration)
• The amplitude contrast (rlnAmplitudeContrast)
• (optional) The path to a STAR file containing the 3D positions of fiducial markers detected by relion_tomo_find_fiducials (rlnTomoFiducialsStarFile)

The tables after that correspond to one tomogram each, and they carry the same name as the tomograms to which they refer. Each row corresponds to one tilt image and describes the following properties:

• The rows of the projection matrices that map points in 3D space onto the 2D image (rlnTomoProj<X/Y/Z/W>)
• The astigmatic defocus (rlnDefocus<U/V> and rlnDefocusAngle).
• The cumulative radiation dose (rlnMicrographPreExposure).

The tomogram set is typically the first data file that is created as part of a new project. It can be generated by importing an existing alignment from IMOD by repeatedly calling the program relion_tomo_add_tomo, once for each tomogram. Each call will add another tomogram to the tomogram set. The initial alignment can and should be later optimised using the relion_tomo_align_frames program. A more detailed description of this is provided in importing tomograms.