Sculpting with Ions

Live exhibit: https://advanced-em.github.io/FIB-view/

An interactive dual-beam microscope (FIB-SEM) in the browser, built as a small science-museum exhibit. It is the sister exhibit of Seeing with Electrons (TEM) and Seeing Surfaces (SEM): everything the SEM exhibit does, plus a focused ion beam that images, mills, deposits and prepares TEM lamellae.

• 3D cutaway dual beam: the electron column and an ion column 52° from it, crossing at the coincidence point; a gallium liquid-metal ion source or an inductively coupled plasma source (xenon, argon, nitrogen, oxygen, with their gas bottles), an aperture strip, gas-injection needles, a lift-out manipulator, the ion detector, and all the SEM detectors (ETD, in-lens, 4-quadrant BSE, EDS, EBSD, TKD). Ions travel visibly slower than electrons, and sputtered atoms fly off the spot. Click any label for an instrument-physics card.
• Thirteen modes:
  • Electron beam: SE · ETD, in-lens, BSE (selectable quadrants), EBSD and TKD with live Hough indexing, EDS.
  • Ion beam: ion image (ion-induced secondary electrons or secondary ions), mill, deposit.
  • Workflows: slice & view (FIB-SEM tomography), lamella (an eight-step TEM lift-out) and cryo lamella (on-grid milling of frozen cells for cryo-electron tomography).
  • Physics: Monte Carlo of electrons (interaction volume) or ions (collision cascades).
• Ion species: Ga⁺ (2.5 nm probes, implants and amorphises), Xe⁺ (fast bulk milling, 1.5 pA–2.5 µA), Ar⁺ (gentle polishing), N⁺ and O⁺ (light; oxygen burns carbon and polymers several times faster and boosts secondary-ion yields). Probe size vs current follows measured columns (source, chromatic and spherical terms, with beam tails), and lower voltage enlarges the probe.
• Imaging with both beams: images are ray-cast through the current, milled surface, so a 52° SEM view sees the face of a cross-section (Pt cap, oxide, copper wiring, tungsten vias, silicon) while the ion view looks into the trench from above. Ion images show dramatic channelling grain contrast, dark oxides and positively charged insulators (switch on the electron flood), and every ion frame sputters the specimen: zoom in on tin spheres and watch them erode.
• Milling physics: sputter yields from measured Ga 30 kV volume yields, scaled to the other species and energies with Sigmund's theory and ZBL nuclear stopping, Yamamura's angular dependence, channelling (grain-dependent milling), gas chemistry (XeF₂ for Si/SiO₂/W, water for carbon), redeposition in deep, narrow trenches, sloped walls and beam tails. Patterns (rectangle, regular cross-section, cleaning cross-section, line, circle) are drawn on the ion image and run one after another; their dose comes from a silicon "application file", so other materials end up deeper or shallower than asked. Curtaining appears below materials of different yield, reduced by a Pt cap and a rocking mill.
• Gas injection: Pt, C and W deposition with the ion or the electron beam, with reaction-limited, precursor-limited and net-milling regimes vs current density.
• Ion collision cascades: a binary-collision Monte Carlo (ZBL potential with a tabulated scattering integral, Lindhard–Scharff electronic stopping, full recoil cascades, surface-binding sputtering): Ga 30 keV in Si gives a projected range of ~27–30 nm and a yield of ~2, as in SRIM.
• Slice & view: a Li-ion cathode (NMC particles with cracks, carbon-binder web, ~30 % pores) or the chip, sliced and imaged (BSE or SE), with orthogonal slices, curtains, pore shine-through, and segmented phase fractions compared with the truth.
• Lamella: e-beam Pt, ion-beam Pt, bulk trenches, cleaning cross-sections, J-cut, lift-out, thinning at currents you choose (with over-tilt), and 5/2 kV polishing. The true thickness wedge, amorphous damage, Ga content, bending and holes are tracked; a 5 kV SEM view of the face shows the thickness the way an operator sees it. Send the finished lamella to TKD.
• Cryo-FIB: a cryo stage (−196 to −100 °C) with a 45° pre-tilted shuttle, copper cooling braids and an anticontaminator, and two frozen-hydrated specimens: yeast cells plunge-frozen in vitreous ice on a holey-carbon gold grid, and a high-pressure-frozen yeast paste for cryo slice & view. Ice and biological matter mill ~4× faster than silicon and charge above ~1.6 kV until sputter coated; the organometallic Pt the cold GIS condenses mills ~10× slower than ice. The cryo lamella workflow: sputter coat, cold GIS, milling angle (stage tilt − 7°), micro-expansion joints, then milling passes you choose down to ~200 nm, and a final coat. The true slab is tracked: thickness and t/λ, the damaged layer on each face (Ga⁺ ~45 nm, Ar⁺ ~30 nm, Xe⁺ ~20 nm, from the collision cascades in ice), devitrification from beam heating or a warm stage, ice contamination growing in real time (×10 without the anticontaminator), bending without relief cuts, and a cryo-ET verdict. The SEM view from above shows the organelles the slab cuts through.
• EDS now sees the implanted beam ions (Ga, Xe, Ar) in milled areas.
• Experiments: cross-section a chip, gallium vs xenon vs oxygen on a battery cathode, channelling contrast, charging, nanograins (EBSD vs TKD), a cryo lamella from a frozen cell, gallium vs argon in ice, and a fly-through.

Everything from the TEM exhibit's infrastructure

• Console and on-screen panel: the TEM-view Console (or any game controller) drives the exhibit through the Gamepad API; the knobs follow the active beam (focus, magnification, beam current along the aperture strip, multifunction: stigmator / beam shift / tilt and stage Z / pattern size, context: voltage, pattern depth, deposit thickness, lamella target, slice thickness). Press V for the on-screen panel (Q/W focus, A/S magnification, Z/X current, H/L and K/J multifunction, O/P context, arrows for the stage, Tab, U to start or stop patterning); pop it out to a second screen. The Console is the TEM-view Console: the same hardware drives both exhibits.
• Training scenarios with hidden truth and telemetry: SEM: focus and stigmate, Ion beam: focus without destroying it (scored on sharpness and on the material your imaging removed), Dual beam: find the eucentric height (the stage Z reading is offset), Lamella: thin to 100 nm and Cryo lamella: 200 nm for cryo-ET (the true thickness is hidden). Consent first; sessions are recorded as fib-view-telemetry/1 (no personal data), can be downloaded, replayed with a scrubber and the true score over time, analysed with tools/analysis/sessions.py, and shared with a Hugging Face dataset through hf/ (a Cloudflare Worker or an HF Space collector, and hf/build_dataset.py for the sessions and steps tables). js/config.js holds the collector address (empty: local only).
• AI mode (brain button, /): a command bar and push-to-talk voice (M) with a FIB grammar ("switch to xenon", "ion current 1 nA", "tilt to 52", "mill a box 10 by 5 by 2 microns", "clean the face", "deposit 1 micron of platinum", "slice and view", "next step", "thin to 100 nm", "polish at 5 kV", "cryo lamella", "sputter coat", "milling angle 12", "mill to 800 nm at 300 pA", "anticontaminator on"), spell correction with confirmation, and analyses: measure_resolution, measure_mill, sputter_yield, fit_eds, ebsd_stats, sv_fractions, lamella_thickness, cryo_quality, ion_range, each compared with the simulator's truth.
• AI agents: is an MCP server: headless , , and tools, and live control of an open exhibit after the visitor clicks (, , , , , , , ). It listens on port 8792 so it can run next to TEM-view's temview-mcp (8790).

Run

ES modules need to be served over HTTP:

python3 -m http.server 8768

Then open http://localhost:8768. Three.js loads from jsDelivr. Plain static files: GitHub Pages works directly.

Releasing

npm test                 # physics references, every mode × specimen, training tasks, grammar
node tools/stamp.mjs     # cache-busting version on every module and the stylesheet in index.html

Regenerate the guide figures and PDFs with node tools/guide-figs.mjs and node tools/guides.mjs, and the icon set and social-preview banner with node tools/icons.mjs (all three use Chrome).

Controls

Drag the instrument to orbit, scroll to zoom. Keys 1–9, 0, -, = switch modes (\ the cryo lamella), Space pauses, C clarity, L labels, R resets the view, N narration, X enlarges the results, V on-screen panel, I acquire, U start/stop patterning, T training, P Python, / AI mode, hold M to talk, [ ] fold the side panels. Drag the image to move the stage (Alt-drag in Mill and Deposit, where a plain drag draws a pattern), scroll it to zoom. In BSE click the quadrants; in EDS click a peak; in EBSD/TKD hover the map for its pattern.

Code map

File	Role
js/physics.js	Electron and ion probes, materials, yields and ranges, sputtering (Sigmund/ZBL/Yamamura), ion-induced SE and SI, binary-collision Monte Carlo, deposition, crystallography, volumetric specimens
js/mill.js	Patterning engine (adaptive per-pattern grids: milling, deposition, imaging damage, redeposition), lamella and cryo lamella workflow models
js/sim.js	Ray-cast imaging for both beams, ion images, EBSD/TKD, EDS, Monte Carlo runners, slice & view
js/ops.js, js/twin.js	The instrument's operations without a page (shared by the UI, voice, agents, Python, headless)
js/render2d.js	Detector views, pattern overlays, curves, orthoslices, lamella views
js/scene3d.js	Three.js dual beam: columns, sources, stage, detectors, GIS, manipulator, beams and particles
js/explain.js, js/components.js, js/narration.js	Explanations, instrument-physics cards, narration
js/panel.js, js/vpanel.js	Hardware panel / game controllers and the on-screen console
js/voice.js, js/agent.js, js/analyze.js	Command grammar, spell correction and confirmation; agent bridge; analyses
js/scenarios.js, js/telemetry.js, js/config.js	Training scenarios, opt-in recorder, deployment settings
js/scripting.js, js/ide.js	Python scripting calls and the in-browser IDE
js/acquire.js, js/export.js, js/npy.js, js/state.js	Acquisitions, NumPy export, session state
hf/	Hugging Face dataset builder and session collectors (Worker, Space)
tools/fibview-mcp/, tools/fibview-py/, tools/headless.mjs, tools/analysis/	MCP server, Python package, headless runner, session analysis
docs/guides/, ,

License

All rights reserved while the licenses for the software, documentation, hardware and firmware are decided. See LICENSE.