SEM Trainer
SE
RED ROI · 2× SCAN
WOBBLE ROI
1 µm
VENTED
CHAMBER OPENBeam disabled — pump down to image
⚠ CHARGING DETECTED
10kV SP=7 WD=10.0 x1500 HV SE
HV: OFF
VAC: 4.2×10⁻⁴ Pa
DET: SE
SCAN: IDLE
X: 0.000 mm | Y: 0.000 mm

IMAGE INFO

Accelerating V— kV
Working Dist.— mm
Magnification×—
Pixel Size— nm
DetectorSE
Scan ModeNORMAL
Dwell Time— µs
Resolution1024×768
Date / Time

BEAM SETTINGS

10
10
3
50
50

WELCOME TO SEM TRAINER

Would you like to run the guided tutorial?

It walks you through every control — beam parameters, focus, alignment, wobble, and more — and ends with you having built a properly-tuned SEM image.

EBSD — ELECTRON BACKSCATTER DIFFRACTION

READY
Pattern Q: 0.00
CI: 0.00
FPS: 0
Indexed: 0%
Time: 0.0 / 45 s
KIKUCHI PATTERN
ORIENTATION MAP (IPF)
Press Start Scan to begin orientation mapping.

EDS — ENERGY DISPERSIVE X-RAY SPECTROSCOPY

READY
CPS: 0
Dead Time: 0.0%
Time: 0.0 / 30 s
Total Counts: 0
Press Acquire to start collecting the spectrum.

SEM TRAINER — USER MANUAL

1. Overview

SEM Trainer is a browser-based simulator that mimics the controls and image behavior of a Scanning Electron Microscope. The sample is a tin-particle preparation on a carbon substrate, rendered procedurally in world-space so it stays sharp at every zoom level. Every control changes the image the way it would on a real instrument: beam energy, focus, stigmation, aperture alignment, scan speed, and so on.

The interface is laid out like a real SEM:

  • Top toolbar — annotation tools, color picker, aperture / wobble / RED, scan modes, Shuffle / Reset / LED, Tutorial / Manual.
  • Left sidebar — opens panels (Condition, Aperture target, Magnifier, Focus, Brightness/Contrast, Camera snapshot, Info).
  • Right sidebar — E-Gun and Vacuum master controls.
  • Center — live SEM viewport. Drag to pan, double-click to center, scroll the imprint bar to change beam parameters.

2. Vacuum Modes

The right-sidebar Vacuum cell is a three-state selector. Pick the mode using the three small buttons (VENT / LV / HV) under the icon. The current chamber pressure shows beneath them and the SVG status box mirrors the active mode.

VENTED (≈ 1 × 10⁵ Pa)

Chamber is open to atmosphere — the sample-exchange state. The E-Gun shuts down immediately, the viewport blacks out with a red VENTED — CHAMBER OPEN overlay, and the beam cannot be re-enabled. Selecting LV or HV from vented triggers the 10-second STARTING VACUUM pump-down screen.

LV — Low Vacuum / ESEM (≈ 10–270 Pa)

Residual gas in the chamber neutralises surface charge on insulating samples — the primary advantage of LV. The image is blurred and slightly de-saturated to simulate beam-skirting through gas. The SE detector is automatically forced to BSE in LV (SE would arc in residual gas), and the trainer will refuse to switch back to SE until you return to HV. kV is clamped to ≥ 10 kV. Insulating samples (Alumina, biological insects, the unknown contamination sample) image cleanly here with no charging artefacts.

HV — High Vacuum (≈ 8 × 10⁻⁵ Pa)

Standard SEM operating mode. Full resolution, full kV range, both detectors available. Insulating samples viewed in HV with the SE detector active trigger a flashing ⚠ CHARGING DETECTED warning in the top-right corner — the typical real-SEM symptom of trying to image an uncoated insulator. Switching to LV or to the BSE detector clears the warning.

Safety interlocks

  • The E-Gun cannot turn on while the chamber is vented.
  • Mode switches during an active pump cycle are rejected — wait for the overlay to finish.
  • Each LV ↔ HV change runs a short pump cycle; venting always runs a 10-second venting cycle.
  • Whenever the E-Gun is off the viewport stays completely black, regardless of scan mode.

3. The Imprint Bar

The semi-transparent bar at the bottom of the image is the live read-out, just like the data strip burned into a real SEM micrograph. Left to right: kV (accelerating voltage), SP (spot size), WD (working distance, mm), x-mag, HV (E-Gun on/off), SE (detector type).

Hover the bar to bring its opacity up. Scroll the mouse wheel on any value to adjust it. Arrow keys work too if you click to focus a value. Clicking HV toggles the E-Gun (subject to the vacuum interlock).

While your cursor is over the imprint, the viewport's zoom-on-scroll is suppressed so you can adjust values without zooming.

4. Beam Parameters

Accelerating Voltage (kV)

The energy of the electron beam. Higher kV (20–30) penetrates further into the sample and improves resolution, but can damage sensitive specimens and reduces surface contrast. Lower kV (1–5) is gentler and surface-sensitive. Trainer default: 10 kV.

Spot Size (SP)

The diameter of the beam at the sample. Smaller spot = sharper image with less signal (noisier). Larger spot = more current and stronger signal but blurrier. Trainer default: 7.

Working Distance (WD, mm)

The distance from the objective lens pole-piece to the sample's focal plane. On a real SEM the focus knob shifts the focal plane up or down, and the WD display reads where that plane currently sits — same model used here. The sample's true WD is randomized between 7.0 and 13.0 mm each session, and you have to focus to bring the focal plane onto it. Each unit of Coarse Focus shifts the WD readout by 0.15 mm; each unit of Fine Focus by 0.015 mm (10× smaller, for the last bit of trim). Scrolling the WD value on the imprint bar moves the coarse focus slider directly.

5. Sample Library

The amber Sample dropdown in the top toolbar (right of User Manual) picks the loaded specimen. Changing the sample re-paints the SE/BSE view and synchronously updates the matching preset in the EDS and EBSD panels.

Materials

  • Tin on Carbon — bright Sn microspheres on amorphous-C film. Classic SEM standard.
  • Stainless Steel 304 — austenitic metal with grain boundaries, twin lines, polishing scratches, and occasional MnS inclusions.
  • Aluminum 6061 — extruded surface with elongated grains, dark Mg₂Si precipitates and bright Fe-rich intermetallic particles.
  • Gold on Carbon — small bright Au islands on carbon film, the classic resolution test.
  • Silicon Wafer — polished single crystal with rare dust / scratches.
  • Pure Copper — FCC grains with annealing twins, pull-out pits, oxidation patches.
  • Alumina Ceramic — equiaxed grains, intergranular pores, bright grain-edge charging. Insulator.
  • NMC Battery Cathode — secondary particles with cauliflower morphology.
  • Unknown Contamination — heterogeneous debris field, mixed brightness, sparse fibres.

Biological — sputter-coated

  • Honey Bee Compound Eye — hexagonal ommatidial array, plumose body setae, corneal nipple nanotexture.
  • Jumping Spider Eye — large smooth principal corneal lens surrounded by sensilla sockets and cuticular ridges.
  • Cockroach Antenna — segmented cuticle with bristle setae, basiconic chemoreceptor pegs, microtrichia, and chemoreceptor pit organs.

Each sample carries a conductivity property (conductor / semiconductor / insulator) that drives the HV-mode charging warning and is used by the EDS / EBSD modules.

6. Condition Setting Panel

Opens from the gear icon. The e-gun fine-tuning controls live here.

ACC Voltage

Type any value 0–30 kV, or click one of the four preset buttons (10, 15, 20, 25 kV). A red-X icon appears while the value is invalid.

Spot Size

Beam diameter setting, integer values.

Filament

Voltage that heats the cathode wire to release electrons. Recommended range 2.0–2.15 V. Above 2.2 V shortens filament life — the simulator notifies you when you cross that threshold. The red marker on the slider track is the recommended zone.

Bias

The voltage that pulls electrons from the filament toward the sample. Bias and filament together drive the emission current.

Emission Current

Live read-out. Target is 80 ± 5 µA. The display turns amber when you're inside the 75–85 µA window. At the trainer's defaults (filament 2.10 V, bias 300 V) you should be right at 79 µA.

7. Brightness & Contrast Panel

Opens from the spoke-gear icon. Two image post-processing controls:

  • Brightness — adds an offset to every pixel; lifts the image up or down.
  • Contrast — multiplies the spread around the midpoint; stretches or compresses the gray-scale.
  • Auto button — resets both to 50 (neutral).

8. Magnification Panel

Opens from the magnifier icon. Direct entry field at the top accepts 1,500×–50,000× (red-X marks out-of-range values). Six amber preset buttons jump to common magnifications (1.5k / 5k / 10k / 20k / 30k / 50k). The Continuous MAG Save checkbox tells the snapshot tool to embed the current mag in the saved filename.

You can also change magnification by scrolling on the x-mag value in the imprint bar (≈8% per tick) or by scrolling anywhere on the viewport (zoom-to-cursor 15% per tick), both clamped to the 1.5k–50k window.

9. Focus & Astigmatism Panel

Opens from the focus reticle icon. The slider position you need to reach for a sharp image is the position where the focal plane sits exactly on the sample — randomized each session (the sample is at a different WD every reload). kV, spot, and any column-alignment error also shift the optimum.

Coarse Focus

Large-step focal-plane adjustment — 0.15 mm of WD change per slider unit. Use this to bracket the sample.

Fine Focus

Small-step trim — 0.015 mm of WD change per slider unit (10× smaller than coarse). Use it for the last bit of sharpness after coarse is dialled in.

Auto Focus

Drives the focal plane directly to the sample's randomized true WD. Sets coarse to the calculated optimum and fine back to 50; the notification confirms the resulting WD (e.g. "Auto-focus complete — WD 11.3 mm"). Equivalent to a real SEM's auto-focus button — useful for recovery after a Shuffle.

Stig X / Stig Y

Astigmatism is when the focused beam is not perfectly round — it's elliptical. Causes: contamination, magnetic fields, dirty apertures. Visually: a strong directional smear (horizontal when Stig X is off, vertical when Stig Y is off). The trainer uses a GPU SVG directional-blur filter so the effect is instant and smooth as you drag. Centering both sliders at 50 removes the filter entirely.

10. Alignment Panel

Opens from the crosshair-target icon.

  • Beam Alignment checkbox — master enable. With it off, the entire column is grossly mis-aligned (large image shift and added blur).
  • Tilt X / Y — gentle scan-coil tilt. Small effect: shifts the image by a few dozen pixels at extremes.
  • Aperture X / Y — physical column-aperture position. Large effect: tens to a couple hundred pixels of image shift. This is the alignment you do with the wobble tool.
  • Live profile graphs — show beam-shape and intensity distribution. They broaden as misalignment grows.

11. Wobble

The wheel icon (to the left of RED) toggles wobble. Wobble modulates the objective-lens current at about 1 Hz. A 540×440 ROI box appears in the center of the viewport showing a live image; if the aperture is mis-aligned, the image inside the ROI visibly swings back and forth. The further off-axis the aperture, the bigger the swing.

How to align with wobble

  1. Turn wobble on.
  2. Watch which direction the image is wobbling.
  3. If it's wobbling in Y (up-and-down), adjust Aperture Y first until the image is only drifting in X.
  4. Then adjust Aperture X until the image looks like it's breathing in place — gently zooming in and out without any side-to-side or up-and-down motion.
  5. When only that breathing motion remains, your aperture is centered.

12. SE & BSE Detectors

The right sidebar now has two detector buttons. The active one glows amber.

  • SE (Secondary Electron) — default surface-topography signal. Strong edge brightening, directional highlight, fine texture, and surface noise. The detector everyone learns SEM on. Disabled while the chamber is in LV (it would arc in residual gas).
  • BSE (Back-Scatter Electron) — atomic-number contrast. Smooth Lambertian dome shading on particles, no edge rim, very dark substrate for low-Z materials and very bright for high-Z. Use BSE for Z-contrast images of polished or insulating samples, and as the only available detector in LV.

Charging warning

Combining HV + SE + an insulating sample (alumina, biological insect specimens, the unknown contamination preset) lights the red ⚠ CHARGING DETECTED badge in the top-right of the viewport. Switch to LV (residual gas neutralises charge) or to BSE (no acceleration of secondary electrons) to clear the warning.

13. RED — Reduced Area Scan

The RED button opens a 540×440 ROI in the center of the viewport that refreshes at 2× the current scan-mode speed. While RED is on, the main image is frozen and every adjustment you make (focus, alignment, brightness, kV, etc.) previews only inside the ROI. When you turn RED off, the full image updates to reflect all the changes you made.

Use RED for rapid focus/alignment tuning when full-frame scans are too slow. Wobble and RED are mutually exclusive — turning on either one automatically disables the other.

14. Scan Modes

UF — Ultra-Fine

30 fps refresh with heavy detector noise (the image looks like TV static dancing on top of the sample). Use for live tuning — you see every adjustment instantly, but quality is low.

TV

7 fps refresh with moderate noise. Middle ground.

SLOW

Zero noise, no auto-refresh. A bright amber scan line sweeps top-to-bottom over 9 seconds, committing the clean image row by row as it passes. This is the SEM equivalent of a slow, high-quality acquisition. If you zoom or change settings during SLOW, only the rows the line has touched since the change reflect the new state — exactly like a real long-integration capture.

15. Alignment LED

Small status light to the right of the Reset button. Color reflects the worst of the eight tunable parameters (coarse focus, fine focus, stig X/Y, tilt X/Y, aperture X/Y):

  • Red — overall score below 80 % of optimum.
  • Yellow — 80–95 %.
  • Green — 95–100 %.

Hover the LED for the exact percentage.

16. Auto Controls Overlay

The bottom-right of the viewport shows an opacity-faded overlay (matches the imprint bar — ~50 % at rest, ~92 % on hover) with three quick-access auto controls, each paired with a fine-trim slider:

  • FOCUS — snaps coarse + fine focus to the calculated optimum (the per-session WD target). The slider next to it nudges coarse focus ±15 units around that optimum.
  • BRIGHT — resets brightness and contrast to 50/50. Slider trims brightness ±25 from neutral.
  • ALIGN — snaps tilt X/Y and aperture X/Y to their per-session optima and re-enables the master Beam Alignment checkbox. Slider trims aperture-X ±10 from optimum for fine-tune practice.

Each auto button resets its companion trim slider to zero so pressing the button brings you back to the calibrated optimum, with the trim available for off-optimum nudges from there. The trims write directly to the underlying state (and to the matching panel sliders), so the Focus / Brightness / Alignment panels stay in lock-step.

17. Shuffle & Reset

  • Shuffle — knocks every alignment parameter 20–40 units off optimum. Image goes blurry, shifted, astigmatic. Training challenge — bring it back.
  • Reset — restores every parameter to its default or per-session optimum: focus to the calibrated optimum, stig to 50, alignment centered, kV=10, spot=7, WD=10, filament=2.10 V, bias=300 V, brightness/contrast = 50, beam alignment on.

18. EDS Module

The right-sidebar EDS button opens the Energy Dispersive X-Ray Spectroscopy panel — a draggable industrial UI with a real-time spectrum graph, status indicators, and sample preset matched to the loaded specimen.

Acquisition controls

  • Sample dropdown mirrors the toolbar selection.
  • Time (1–600 s) — acquisition window.
  • Acquire starts the scan; counts accumulate Poisson-sampled in 1024 energy bins over the configured window. Stop halts mid-scan; Reset zeros the spectrum; Auto ID identifies preset elements from the live spectrum; Export CSV saves a JH-named CSV.
  • Status bar shows CPS, dead-time %, FPS-equivalent timer, and a running total-counts readout.

FOV-aware composition

Peak intensities scale with what is currently visible in the viewport, not the bulk preset ratio. Particle-bearing samples (Tin-on-Carbon, Gold-on-Carbon, NMC) interpolate between a particleElements composition and a substrateElements composition by counting bright pixels inside the viewport. Zoom into a single tin sphere and the spectrum is nearly pure Sn; pan to a bare carbon patch and you read mostly C. Single-phase samples (Si, Cu, ceramics, biologicals) use their bulk composition unchanged.

Auto ID

Searches a bremsstrahlung-subtracted "net" spectrum for peaks above a noise floor, then matches each preset element's characteristic lines (within ±2.5 bins) to find which ones actually fired. Only elements that are in the loaded preset are considered — so a Tin-on-Carbon scan can never accidentally report Boron. Lines whose energy exceeds 95 % of the current beam kV are also skipped (the beam can't excite them). The chip readout sorts by net peak height and shows estimated weight-%.

Clicking anywhere on the spectrum identifies the closest characteristic line and pops a notification with the element / line / energy.

19. EBSD Module

The right-sidebar EBSD button opens the Electron Backscatter Diffraction panel — a draggable dual-pane workspace showing a live Kikuchi pattern viewer and an Inverse Pole Figure orientation map. Sample preset stays synchronised with the toolbar selection.

Status bar

A color-coded LED (Ready / Acquiring / Indexing / Calibrating / Done / Error) plus live Pattern Quality, Confidence Index, FPS, indexed-percentage, and timer readouts.

Kikuchi viewer

Pattern bands are procedurally generated per material with deterministic seeding (so the same sample always shows the same band pattern). Subtle per-frame drift simulates a live camera; per-frame speckle noise scales with the Gain slider and is attenuated by Exposure and Binning — exactly how a real EBSD camera responds. Pattern Quality is derived from the gain/exposure balance.

Orientation map (IPF)

Voronoi-seeded grains painted with vivid IPF-style hues. As the scan runs, pixels fill in left-to-right top-to-bottom at a rate that completes within the configured time. Grain boundaries render near-black, un-indexed pixels render dark grey. Frequency of un-indexed pixels is driven by per-material indexability: 0.98 for silicon, ~0.92 stainless, down to ~0.04 for biological / amorphous samples. Single-crystal samples (Si) paint as one uniform IPF color; amorphous samples (insect cuticle, tin/gold-on-carbon) produce mostly noisy non-indexed greyness with rare random hits.

Click any grain after the scan completes to get fake Euler angles (φ₁, Φ, φ₂) and a per-grain CI. Calibrate runs a 2.2 s pattern-scrambling animation. Export PNG saves the orientation map.

20. Annotation Tools

The top-toolbar icons (after the cursor) draw on the viewport overlay:

  • Line — drag to draw.
  • X-cross marker — single click.
  • Plus crosshair — single click.
  • Triangle — drag to draw.
  • Rectangle — drag to draw an outlined rectangle.
  • Filled circle — drag for a filled disc.
  • Ring — drag for an outline circle.
  • T (text) — click, you'll be prompted for the text.
  • Eraser — click an existing annotation to remove it.

The multicolor orb opens a 10-color palette popup. Pick a color to use for any new annotation; the orb's bottom edge tints to the current color.

21. Snapshot

The camera icon in the left sidebar saves a PNG of the visible viewport with the current CSS filter baked in (focus blur, brightness/emission). The filename uses the product name and the current date, e.g. JH Technologies SEM Trainer 2026-05-11.png.

22. Mouse & Keyboard Shortcuts

  • Scroll wheel on viewport — zoom in / out (15% per tick).
  • Drag in viewport — pan the view (when the pointer or precision-select tool is active).
  • Double-click in viewport — center the view on the clicked point.
  • Scroll wheel on imprint value — adjust that value (kV ± 0.5, SP ± 1, WD ± 0.1, mag ± 8 %).
  • Scroll wheel on any slider — adjust the slider by 1 % of its range per tick.
  • Arrow keys on focused imprint value — fine adjust.

23. Tutorial

The Tutorial button (right of the alignment LED) launches a 30-step contextual walkthrough. It starts by deliberately disturbing every parameter, then walks you through every control in order, gated by an action at each step. By the time you reach the final step, every parameter is back to its optimum / default and you've built a properly-tuned image. You can replay it any time — the button stays in the toolbar for a refresher.

JH SEM ACADEMY

Introduction to Electron Microscopy — a technician-readiness program built on the COXEM EM-40

SEM TRAINER

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One-time activation; an internet connection is required only for this step.
JH Technologies, Inc. — Fremont, CA · Need access? Contact your instructor or JH Technologies.
PUMPING DOWN
Coming to vacuum pressure…

Brightness/Contrast Control
Brightness
+
Contrast
+
Magnification
Alignment
X +
Y +
X +
Y +
0.2 0.15 0.1 0.05 0 0 50 100 150 200 250 60000 50000 40000 30000 20000 10000 0 0 500
Condition Setting
ACC Voltage
Spot Size
Filament 0.00V
+
Bias 0V
+
Emission Current E-Gun OFF
Focus
Coarse Focus
+
Fine Focus
+
Stig X
+
Stig Y
+