DASAPT

User documentation

APT Calibrator

A practical guide to installation, the AP Suite workflow, and the four core modules described in Chen et al., Microscopy and Microanalysis (2025).

1. Installation

APT Calibrator is a standalone Windows application. It does not require AP Suite to launch, but most calibration workflows exchange data with AP Suite 6.x.

Run the installer, then open APT Calibrator from the Start menu. The main menu lists ICF calibration, kf calibration, pole-figure simulator, runtime calculator, and dynamic reconstruction.

Overview of APT Calibrator

Initialization fields typically include flight path, lattice constants, crystal structure, and an initial tip radius. The radius can come from TEM/SEM, or from an empirical starting guess that is refined later.

2. File formats and AP Suite

Two interaction modes are supported.

Standard calibration

  1. In AP Suite, use Reconstruction Wizard / Reconstruction Explorer to generate detector hit maps and spatial distribution maps.
  2. Index poles and measure plane spacing as described below.
  3. Enter the measured values in APT Calibrator to obtain ICF and kf.
  4. Reapply those parameters in AP Suite and rebuild the reconstruction.

Correlative dynamic reconstruction

  1. Perform a rough reconstruction in AP Suite.
  2. Export .apt and convert to .epos (ion sequence, voltage, mass-to-charge, detector coordinates).
  3. Load the dataset in APT Calibrator and place golden seeds against TEM/STEM/4D-STEM fiducials.
  4. Compute depth-resolved ICF and kf.
  5. Either reimport parameters into AP Suite, or reconstruct in APT Calibrator and export .pos.

3. ICF calibration

Image compression factor ξ is obtained from crystallographic poles on the detector hit map (Gault et al., 2008, 2009):

ξ = θcrys / θobs

θcrys is the theoretical angle between Miller indices. θobs is the observed angle from pole coordinates on the detector divided by the flight path. The software uses an equidistant azimuthal / Hawkes–Kasper angular magnification scheme.

  1. Open a detector hit map and identify at least two poles. The pole-figure repository and simulator in Tools help assign Miller indices, including signs.
  2. Enter Miller indices and detector coordinates (x, y) for each pole.
  3. APT Calibrator returns the ICF.
Calibrate ICF from crystallographic poles

Symmetry-equivalent index sets depend on the projection axis. Use the pole-figure simulator to rotate the crystal until the overlay matches the hit map before locking the assignment.

4. Standard kf iteration

Field factor follows from a calibrated apex radius:

F = V / (kf R)

  1. Choose an initial tip radius, typically 20–100 nm, such that spatial distribution map peaks are visible in AP Suite.
  2. Measure observed interplanar spacing at a selected pole (for example Al (111) = 0.234 nm theoretically).
  3. Enter the observed spacing. The software updates the radius so that reconstructed spacing approaches the theoretical value (Ceguerra et al., 2019).
  4. Rebuild the spatial distribution map with the new radius and repeat until spacing converges.
  5. Combine the converged radius with evaporation field F (tabulated, Müller / Brandon charge-state selection) and the initial voltage V to obtain kf.

The reconstruction of atoms at the pole for the z-direction spatial distribution map is documented in supplementary videos S1 and S2 of the paper.

5. Pole-figure simulator

The simulator uses an azimuthal equidistant projection, which is more appropriate for APT than the gnomonic projection used in EBSD-style Hough indexing.

  • Inputs: crystal structure, lattice constants, plane-spacing threshold Dplane, flight path, ICF, and Bunge–Euler angles.
  • Lower Dplane shows more zone lines (for example 0.10 nm vs 0.15 nm).
  • Quick settings: LEAP 5000 XS (straight flight path) and LEAP 5000 XR (reflectron). Enable the Reflectron checkbox for XR; detector size and mounting angle differ.
  • Angle correction aligns the sample reference frame with the detector hit map, which is often rotated by stage and detector mounting.
  • Euler angles may be typed manually or taken from TKD or EBSD. Grain orientations can be stored with Save Grain to compute misorientation angle and rotation axis, including screening for low-Σ CSL boundaries.

Newer instruments (LEAP 6000 XR, Invizo 6000) can be approximated by updating detector size, projection geometry, and field of view. Lens-edge distortions on Invizo are not corrected; that would require Cameca’s proprietary mapping.

Pole-figure simulation in APT Calibrator

6. Golden-seed dynamic reconstruction

ICF and kf change with shank angle, radius, and evaporation sequence. When poles or lattice spacing are unavailable, fiducials from TEM/STEM still constrain depth scaling.

  1. Start from a static reconstruction (example values in the paper: ICF = 1.5, kf = 3 for Sm–Co–Cu–Zr; ICF = 1.65, kf = 1.25 for Fe–1W).
  2. Place several golden seeds on distinctive features in both the APT volume and the STEM/TEM image (phase boundaries, precipitates, grain-boundary junctions).
  3. Compare inter-seed distances versus depth. Systematic scaling error is converted into a depth-dependent correction of kf/ξ.
  4. Using the empirical relation kf* ∝ (ξ*)3, separate depth profiles of kf(Z) and ξ(Z).
  5. Rebuild. Depth (flight direction) should then match the STEM geometry. Only the central APT field of view is reconstructed; the TEM periphery often lies outside the ion collection angle.

APT Calibrator adopts the Gault protocol for dv/dz rather than a simple reverse-projection area. The Hatzoglou dynamic-voltage protocol used in AP Suite is also available for comparison. In an Al–Mg–Fe example, dynamic kf reduced deviation from theoretical (111) spacing by about 20%.

Dynamic reconstruction with golden seeds

7. Limitations

  • Trajectory aberrations are not corrected.
  • Evaporation field F is still a nominal input; heterogeneous or coated tips can vary by tens of V/nm.
  • Pole-based ICF is only available when crystallographic contrast is resolved.
  • Golden-seed alignment mainly constrains the specimen z-axis; small rotations about z have limited effect but should still be checked.

8. Citation

Chen X, Li Y, Woods E, Zhou X, Gault B. APT Calibrator: A Multifunctional C# Software Application for Reconstruction Calibration in Atom Probe Tomography. Microscopy and Microanalysis. 2025;31:ozaf092. doi:10.1093/mam/ozaf092

Supplementary videos and figures: same DOI. Source code: https://github.com/xinren1230/APT-calibrator.

Corresponding authors: Xinren Chen (x.chen@mpi-susmat.de) and Baptiste Gault (b.gault@mpi-susmat.de).