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apt-profile-2d

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Actualizado24 de junio de 2026 a las 13:55

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.

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peterfelfer

peterfelfer/Atom-Probe-Toolbox

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SKILL.md

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name	apt-profile-2d
description	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.
argument-hint	[species]

Build a 2D concentration map by binning the tip into pixels over two distance axes and computing the composition of each pixel, then displaying a heat map for one species. Use the MATLAB MCP server.

Prerequisites

The MATLAB workspace must contain:

pos — ranged/allocated atom probe data with an ion/atom column (from /apt-composition)

If pos has no ion column, tell the user to run /apt-composition first (ranging + posAllocateRange).

Steps

1. Choose the two distance axes and create bin vectors

dist = [pos.y, pos.z];        % the two coordinates to bin (one column each)
bin  = [1 1];                 % bin width [dim1 dim2] in nm; non-isometric bins allowed
mode = 'distance';            % 'distance' is the only supported mode in 2D
[binCenters, binEdges] = binVectorsFromDistance(dist, bin, mode);

bin sets the pixel resolution and strongly affects compute time — 1 to 2 nm is reasonable. Pick the axis pair the user wants: [pos.x pos.y], [pos.x pos.z], or [pos.y pos.z].

2. Voxelise the data

startIdx = 1;                 % first ion hit index to include
endIdx   = height(pos);       % last ion hit index (must be > startIdx)
pix = posNdBin(pos(startIdx:endIdx,:), dist(startIdx:endIdx,:), binEdges);  % cell array of pos subsets (pixels)

By default include all atoms (startIdx = 1, endIdx = height(pos)). Use a narrower index range only if the user wants to restrict the hit range.

3. Define the concentration kernel (set detection efficiency)

detEff          = 37;             % detector efficiency, percent or decimal both accepted
excludeListConc = {'unranged'};   % species ignored in the composition, optional
volumeName      = '';             % volume label, optional
concentrationKernel = @(pos) posCalculateConcentrationSimple(pos, detEff, excludeListConc, volumeName);

The detection efficiency is critical for correct composition and must match the instrument: 37 (LEAP 4000X HR), 52 (LEAP 5000 XR), 80 (LEAP 5000 XS), 50 (EIKOS). If the user has not confirmed their instrument, ask before proceeding. Read it from config if available: cfg = APTConfig.getInstance(); detEff = cfg.reconstruction.detectionEfficiency*100;.

4. Compute concentration for every pixel

conc = cellfun(concentrationKernel, pix, 'UniformOutput', false);

This applies the kernel to each pixel, producing a concentration (plus count and variance) table per pixel. Composition therefore carries counting statistics per pixel (see concentrationUncertainty).

5. Build and display the heat map for one species

wantedSpecies = cellfun(@(pos) pos.Al(pos.format == 'concentration'), conc);  % replace Al with element/complex ion
figure;
concentrationMap = imagesc(binCenters{1}, binCenters{2}, wantedSpecies);
axis equal;

Set the species to the element or complex ion the user asked for (parse $ARGUMENTS); default to a major solute if unspecified, and tell the user which one you picked. Add colorbar; xlabel('nm'); ylabel('nm'); if helpful.

6. (Optional) Counting uncertainty

counts = cellfun(@(x) sum(x.counts), conc);
unc = concentrationUncertainty(counts);

Sparse pixels (few atoms) have large statistical uncertainty — increase bin to average more atoms per pixel if the map is noisy.

Report

Tell the user the axis pair and bin sizes used, the detection efficiency applied, and which species is mapped, and that a 2D heat map figure was created. Note that pixel composition carries counting uncertainty (larger bins = smoother, less noisy maps). Suggest:

/apt-roi to restrict the map to a region of interest before re-running
/apt-profile-1d for a 1D concentration profile along a single axis
Re-run step 5 with a different wantedSpecies to map another element
Export the figure with exportgraphics(gca, 'concentration_map.png')

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dist = [pos.y, pos.z]; % the two coordinates to bin (one column each) bin = [1 1]; % bin width [dim1 dim2] in nm; non-isometric bins allowed mode = 'distance'; % 'distance' is the only supported mode in 2D [binCenters, binEdges] = binVectorsFromDistance(dist, bin, mode);

startIdx = 1; % first ion hit index to include endIdx = height(pos); % last ion hit index (must be > startIdx) pix = posNdBin(pos(startIdx:endIdx,:), dist(startIdx:endIdx,:), binEdges); % cell array of pos subsets (pixels)

detEff = 37; % detector efficiency, percent or decimal both accepted excludeListConc = {'unranged'}; % species ignored in the composition, optional volumeName = ''; % volume label, optional concentrationKernel = @(pos) posCalculateConcentrationSimple(pos, detEff, excludeListConc, volumeName);

wantedSpecies = cellfun(@(pos) pos.Al(pos.format == 'concentration'), conc); % replace Al with element/complex ion figure; concentrationMap = imagesc(binCenters{1}, binCenters{2}, wantedSpecies); axis equal;