---
title: "STEM-in-SEM: Through a Thin Specimen Interactive Lab | Sandbox Physics"
description: "How thin must a specimen be for a useful SEM transmission image?"
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last_modified: "2026-10-27"
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E24 · Low-voltage transmission

# STEM-in-SEM: Through a Thin Specimen

**How thin must a specimen be for a useful SEM transmission image?** Thin enough that a good share of the electrons gets through at the low beam energy you have chosen. A thicker foil lets fewer through and blurs the image more. The detector collection angles then decide which transmitted electrons form the contrast.

Choose the beam energy, foil thickness and collection angles. Learn to tell weak transmission, probe blur and counting noise apart.

> Interactive simulation: open this page in a web browser to change the parameters and run the model.

Model assumptions

The counts are synthetic and come from a fixed random seed; they are not experimental data. A 32 by 32 raster stores 125 radial bins of 2 mrad at each point. Electrons that land outside this window, and electrons removed from the beam, are simulated and counted separately. The uniform disk of incident angles, the isotropic Gaussian spread of scattered electrons and the empirical attenuation lengths are teaching assumptions, not calibrated cross sections. A stated Gaussian probe blurs the finite specimen before counting. The labels BF, ABF and ADF describe only the collection angles: coherent phase contrast, dynamical diffraction, channeling and real ABF imaging of light atoms are not solved. Changing the virtual angles reuses the stored counts, and display gain never changes the numbers. Contrast is measured in regions fixed in advance; this is not elemental quantification. The hardware, the thickness and the lateral size of the specimen are each enlarged by a different amount. The apparatus shows one representative point on the axis and ignores nanometre scan movements. The SEM beam energy runs from 5 to 30 keV, with a 2 nm raster pitch over 64 nm. The carbon-like wedge varies from 0.6 to 1.4 times the chosen thickness and contains an invented inclusion of atomic number 29.

Physics tutorial

## STEM-in-SEM: Through a Thin Specimen

**Background** To make a transmission image in an SEM, you choose the beam energy, the foil thickness and the collection angles. When the image is poor, you then work out whether weak transmission, probe blur or counting noise is to blame.

**Why it matters** The task is to see the inclusion in transmission. Collect from zero angle. Reach a dark inclusion contrast of at least 0.1, a pooled region difference SNR of at least 10 and a transmitted fraction of at least 30 percent at the selected point, with an assumed probe FWHM of at most 5 nm.

Start with the essentials

- **Focus question**: How thin must a specimen be for a useful SEM transmission image?
- **One-sentence intuition**: The angle range you choose decides which of the stored electrons make up the image.

### Core mathematical model

#### Counts in angular bins

$$
\begin{aligned}\mu_j&=\frac{I\tau}{e}\,p_j\\N_{\rm ann}&=\sum_{j\in\mathcal A}N_j\end{aligned}
$$

Each virtual image adds up the stored radial counts in its chosen angular interval. The interval includes its lower edge but not its upper edge.

#### Assumed angular spread of scattered electrons

$$
\begin{aligned}f(\theta)&=\frac{\theta}{s^2}\,e^{-\theta^2/(2s^2)}\\r&=L\tan\theta\end{aligned}
$$

The isotropic Gaussian radial law stands in for a real transport calculation. The radius on the collector follows from the angle through the collector geometry shown on screen.

#### Contrast and noise in two known regions

$$
\begin{aligned}C&=\frac{\overline N_2-\overline N_1}{\overline N_2+\overline N_1}\\\sigma_\Delta^2&=\frac{\sum_1N}{n_1^2}+\frac{\sum_2N}{n_2^2}\\S&=\frac{|\overline N_2-\overline N_1|}{\sigma_\Delta}\end{aligned}
$$

This pooled difference uses the count statistics of two regions fixed in advance. It is not a per-pixel SNR, and it does not recover composition.

### Common difficulties

#### A bright pixel is not a chemical analysis

**Typical misconception** Any annular image tells me directly which atoms are there.

**Better mental model** Thickness, the range of collected angles and probe overlap also change contrast. Phase effects at low angles need a coherent wave model, which this Lab does not include.

### Run the experiment

1. 01

   #### Predict the contrast

   Compare the separate specimen input with the bright-field image and the image from your selected angles.

   **What to observe:** The known regions are there to check contrast. They are not a recovered chemical map.

2. 02

   #### Change the collection angles without re-acquiring

   Change the inner and outer angles while watching the native histogram and the outcome totals.

   **What to observe:** The virtual images change, but the native radial counts stay the same.

3. 03

   #### Try a setting that works

   Use the Resolve the thin specimen preset and check the target. Compare the row profiles built from the counts.

   **What to observe:** Read the signed contrast and the pooled difference SNR together.

4. 04

   #### Find the limits

   Try low exposure, a broad probe and reversed bounds. Then increase the specimen thickness.

   **What to observe:** Gain changes how the image looks. It cannot put back counts that were never collected or sharpen a blurred probe.

Physical conclusion

To interpret contrast, look at the counts, the collection angles and the probe width together.

Fields & matter · Starter path

## From a field to an electron microscope

Map an electric field and steer a charged particle. Then find the electron's wavelength and use electron beams to see a crystal and a surface.

[Start here → **Make an Electric Field Visible** Move the probe around a dipole and check that the field always points downhill on the potential landscape. Observe · 8 min](https://sandboxphysics.com/labs/electric-field/)

1. [1 Make an Electric Field Visible](https://sandboxphysics.com/labs/electric-field/)
2. [2 A Charge Bending through Fields](https://sandboxphysics.com/labs/charged-particle/)
3. [3 Electron Wavelength & Voltage](https://sandboxphysics.com/labs/electron-wavelength/)
4. [4 Electron Diffraction & Reciprocal Space](https://sandboxphysics.com/labs/electron-diffraction/)
5. [5 TEM Bright Field, Dark Field & SAED](https://sandboxphysics.com/labs/tem-mode-selector/)
6. [6 SEM Secondary-Electron Topography](https://sandboxphysics.com/labs/sem-topography/)

[View the full path →](https://sandboxphysics.com/topics/fields-and-matter/#starter-path)