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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.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
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.
| name | apt-analyze |
| description | 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. |
| argument-hint | <file.pos|file.epos> |
Run a complete atom probe analysis pipeline. Use the MATLAB MCP server.
The file to analyze is: $ARGUMENTS
If no file is provided, ask the user for the file path.
setupToolbox;
load('isotopeTable_naturalAbundances.mat');
load('colorScheme_default.mat');
cfg = APTConfig.getInstance();
Before proceeding, ask the user which instrument acquired this data:
Apply the preset:
cfg.applyInstrumentPreset('LEAP5000XR'); % adjust based on answer
pos = posLoad('$ARGUMENTS');
fprintf('Loaded %d atoms\n', height(pos));
spec = massSpecPlot(pos, 0.01, 'normalised');
Ask the user what elements they expect in their sample (e.g., "Fe, C, Mn" for steel). Then add ion markers:
ionAdd(spec, 'Fe', 2, isotopeTable, colorScheme);
ionAdd(spec, 'C', 1, isotopeTable, colorScheme);
% ... for each element at likely charge states
Tell the user to check the spectrum in MATLAB and confirm the ion identification looks correct. Then:
rangeAddAll(spec, colorScheme, 0.04, true);
rangeTable = rangesExtractFromMassSpec(spec);
pos = posAllocateRange(pos, rangeTable, 'decomposed');
detEff = cfg.reconstruction.detectionEfficiency;
conc = posCalculateConcentrationSimple(pos, detEff, {'unranged'}, '', 'mode', 'atomic');
unc = concentrationUncertainty(conc.counts);
disp(conc);
scatterPlotPosWidget(pos, colorScheme);
Present a summary: