Atom-Probe-Toolbox

Voronoi-cell cluster determination (Felfer et al. 2015) — detect and extract clusters via Voronoi-cell volumes, Delaunay triangulation, and a Kolmogorov-Smirnov test against a randomised reference. Use when the user wants the Voronoi/clusterDetermination method specifically (this is NOT DBSCAN — for density-based DBSCAN use /apt-cluster instead).

Create a new ion color scheme or add ions/colors to the existing one. Produces/updates the `colorScheme` workspace variable used by ranging and 3D visualization everywhere else. Use when the user wants custom ion colors, a new color scheme, or to add a missing ion color.

Per-vertex concentration mapping onto a mesh/interface — compute atom-to-mesh distances, clip a slab around the interface, voxelise by nearest vertex, and apply a concentration kernel to colour each vertex. Use when the user wants a concentration map painted onto an isosurface or modelled grain boundary mesh.

Run quality-control checks on an atom probe dataset before analysis — basic stats, voltage curve, detector hit map (FDM), mass spectrum sanity, coordinate ranges, multi-hit fraction, and automated quality metrics. Use when the user wants to assess data quality or sanity-check a reconstruction.

Create a field desorption map (detector hit-density / concentration image) and optionally a movie of detector activity over the course of the experiment. Use when the user wants an FDM, desorption map, detector image, or to watch features evolve during the measurement.

Quantify interfacial excess (Gibbsian excess of solute, in at/nm^2) across an interface — either a single value via the Krakauer-Seidman integral method, or a 2D excess map over the surface. Use when the user wants the amount of an element segregated to an interface or grain boundary.

Full pipeline from voxelisation through proxigram — voxelise, build an isoconcentration surface, then compute single- and multi-ion proxigrams across it in one guided sequence. Use when the user wants a proxigram but does not yet have an interface.

Voxelise atom probe data, compute a concentration field, and render a 3D isosurface at a chosen at.% threshold (e.g. for interfaces, precipitates, or grain boundaries). Use when the user wants an isoconcentration surface or isosurface from their APT data.

Load an IVAS-style .rrng (or .rng) range file onto an existing mass spectrum, recreating all its ion ranges (and their colors) on the plot. Use when the user has a .rrng/.rng file and wants to apply those ranges instead of defining them by hand.

Automated mass spectrum analysis — peak detection, ion identification by isotopic pattern matching, and auto-ranging (EER). Use when the user wants ions and ranges found automatically instead of picking them by hand (contrast with the manual /apt-spectrum).

Background-corrected peak counting — fit a linear background under a single mass-spectrum peak from interactively brushed bins and get its corrected counts/percentage. Use when the user wants accurate peak counts with background subtraction, signal-to-background, or to build a table of corrected peaks.

Compute and plot a 1D concentration profile (composition vs. distance) from ranged/allocated atom probe data by voxelising along one axis. Use when the user wants a concentration profile, line profile, or composition-along-z plot.

Compute and display a 2D concentration map (heat map of one species over a plane) from ranged/allocated atom probe data by voxelising along two axes. Use when the user wants a 2D concentration map, composition heat map, or chemical map.

Compute a proximity histogram (proxigram) — concentration vs. distance from an existing interface (isosurface, line, or point cloud) — for one or many species. Use when the user has an interface and wants a concentration profile across it.

Reconstruct 3D atom positions (x, y, z) from detector hit coordinates and the voltage curve using the Gault et al. straight-flight-path algorithm. Use when the user wants to reconstruct, build, or recompute the 3D point cloud from raw detector data.

Define a region of interest (box, cylinder, sphere, or plane) on a 3D atom probe reconstruction, crop the data inside it, and plot a 1D concentration profile along the ROI axis. Use when the user wants to select, crop, or analyze a local sub-volume of their APT data.

Run a full atom probe analysis pipeline on a data file. Loads data, creates mass spectrum, and guides through ion identification, ranging, and composition calculation. Use for end-to-end APT analysis.

Run DBSCAN cluster analysis on atom probe data. Use when the user wants to find clusters, precipitates, or perform cluster analysis.

Calculate the composition (concentration) of atom probe data. Handles range extraction, ion allocation, and concentration calculation. Use when the user asks about composition, concentration, or chemical analysis.

Load an atom probe data file (.pos or .epos) and display summary statistics (atom count, coordinate ranges, mass-to-charge range). Use when the user wants to load or open APT data.

Initialize a MATLAB session for atom probe analysis. Run this at the start of every APT session to set up the toolbox, load isotope tables, and load the default color scheme.

Create a mass spectrum from loaded atom probe data and optionally identify ions. Use when the user wants to see or analyze a mass spectrum.

Create a 3D scatter plot visualization of atom probe data. Use when the user wants to see a 3D view, atom map, or point cloud of their APT data.