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 a single table, named global, which 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 trajectory set)

  • The tilt series file name (rlnTomoTiltSeriesStarFile): the path to the star file corresponding to each tomogram/image stack

  • 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 raw micrographs, given in Å (rlnMicrographOriginalPixelSize)

  • The pixel size of the tilt series, given in Å (rlnTomoTiltSeriesPixelSize), corresponding to the dimensions given by rlnTomoSize<X/Y/Z>, after the binning applied in the Motion correction job

  • The tomogram binning (rlnTomoTomogramBinning): the binning applied to the tilt series in rlnTomoTiltSeriesStarFile to reconstruct the tomogram in rlnTomoReconstructedTomogram

  • The reconstructed tomogram file (rlnTomoReconstructedTomogram): the path to the reconstructed tomogram mrc file, at the binning in rlnTomoTomogramBinning

  • The Etomo file (rlnEtomoDirectiveFile)

  • The optics group name (rlnOpticsGroupName)

  • The voltage, given in kV (rlnVoltage)

  • The spherical aberration, given in mm^-1 (rlnSphericalAberration)

  • The amplitude contrast (rlnAmplitudeContrast)

The star file for each tomogram, to which rlnTomoTiltSeriesStarFile points, contains a single table with the same name as the tomogram. In it, each row corresponds to one tilt image and includes the following properties, among others:

  • The tilt image rotation angles and shifts (rlnTomo<X/Y>Tilt, rlnTomoZRot and rlnTomo<X/Y>ShiftAngst)

  • The astigmatic defocus (rlnDefocus<U/V> and rlnDefocusAngle)

  • The intensity scale factor related to effective ice thickness at each tilt angle (rlnCtfScalefactor)

  • The cumulative radiation dose (rlnMicrographPreExposure)

  • The frame count (rlnTomoTiltMovieFrameCount)