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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.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
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-visualize |
| description | 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. |
| argument-hint | [ions to show] |
Create a 3D scatter plot of the atom probe data. Use the MATLAB MCP server.
The MATLAB workspace must contain:
pos — loaded atom probe data, ideally with ions allocated (has ion column)colorScheme — color scheme for ion coloringIf pos has an ion column (ranges have been allocated):
scatterPlotPosWidget(pos, colorScheme);
This opens an interactive widget where the user can toggle ion visibility, rotate, zoom, and adjust transparency.
If pos does NOT have an ion column yet (no ranges allocated), use the basic scatter plot:
scatterPlotPosData(pos, colorScheme);
Tell the user: