RHEED

RHEED (Reflection High-Energy Electron Diffraction) analysis automatically extracts and quantifies diffraction features from RHEED videos and images. It supports stationary stages, rotating stages, and real-time streaming from desktop integrations, screen capture, or custom SDK acquisition. For rotating recordings, the pipeline automatically detects the rotational period, identifies high-symmetry reference frames, and applies per-rotation corrections so that metrics are extracted consistently at each azimuthal angle.

Overview

The RHEED pipeline processes data in three stages:

Data cleaning and standardization: auto-classifies the recording type (stationary vs. rotating), crops to the illuminated region, corrects detector orientation, and for rotating recordings, detects the rotational period and aligns each rotation cycle to consistent azimuthal positions
Pattern extraction: segments diffraction features using deep learning models and quantifies morphological metrics per feature
Timeseries analysis: tracks how extracted metrics evolve across video frames, detects transitions, and identifies changes in surface structure

Key Metrics

Metric	What It Tells You
Lattice spacing	Derived from reciprocal-space feature spacing; in pixels until calibrated, then in Å. Tracks surface reconstruction changes.
Strain	Relative change in diffraction feature spacing over time, calculated from horizontal spacing between neighboring patterns.
Oscillation period	Period of specular intensity oscillations, related to deposition rate.
Spot count	Number of diffraction features per frame. Changes indicate phase transitions, reconstructions, or target thickness reached.
FWHM	Full width at half maximum of specular and first-order spots.
Intensity	Integrated intensity of specular, half-order, and first-order reflections.

For rotating RHEED data, the pipeline automatically detects the rotational period, identifies high-symmetry reference frames, and aligns each rotation cycle before extracting metrics per azimuthal angle. This corrects for variations in rotation speed and ensures equivalent positions are compared consistently across cycles.

Guide
Technical Details

Adding RHEED Data

Choose the acquisition method that fits the instrument:

Desktop integration: use RHEED Camera (GenTL) on the instrument workstation. Open Documentation in the desktop app for camera setup, then see Finding Collected Data. The integration controls collection; viewing a growth does not start a second acquisition.
Upload: add recorded videos or images through Manual Upload.
Custom acquisition: use Stream RHEED to send frames from your own Python application.

Browser screen capture

Use Screen Capture when the source is a RHEED display. That reference covers source selection, capture settings, and pause, resume, and end behavior for browser capture. Gateway recordings are controlled through their integrations, not browser capture settings.

Viewing Results

Once processing completes (or during a live stream), the RHEED workspace shows several sections:Video player: Scrub through the recorded or live video. Reference frame positions are highlighted on the scrub bar for rotating recordings. You can jump to a specific frame number or drag the scrubber to isolate a moment in time.Growth analysis chart: The main analysis view. Select which timeseries to plot (lattice spacing, strain, intensity, FWHM, spot count, oscillation period) and choose the azimuth angle for rotating data. Changepoints appear as shaded bands when the detected surface reconstruction changes (see Technical Details).Saved patterns: Extract individual frames for detailed fingerprint analysis. Click Save Frame to extract the current video frame. Each saved frame shows the fingerprint overlay with extracted diffraction features, intensity maxima positions, and horizontal spacing between the specular spot and nearest features.

Azimuth Calibration

For rotating RHEED recordings, the pipeline automatically detects the rotational period and identifies high-symmetry reference frames. You can refine these in the azimuth calibration panel:

Label azimuths with crystal orientation names (e.g., Al[100])
Unit Calibration: enter a spacing in pixels (Relative Units) and the known distance it corresponds to (Real Units, in nm, Å, or px). Lattice spacing is then reported as a real-space value in Å instead of pixels.

Reanalysis

If you need to adjust analysis parameters, open the workflow configuration drawer to update reference frames or rotational period, then re-run the pipeline.

Comparing Patterns

Save multiple frames and use the pattern comparison tools to view fingerprint overlays side by side or generate difference masks between two patterns. This is useful for identifying subtle changes in surface structure across a growth run.

Analysis Pipeline

The RHEED pipeline processes data through three stages, followed by transition detection.

Stage 1: Data Cleaning and Standardization

Raw RHEED recordings are prepared for analysis. The pipeline auto-classifies the recording as stationary or rotating, crops to the illuminated pattern region, corrects detector orientation, and normalizes intensity across recordings.For rotating recordings, the pipeline automatically detects the rotational period, identifies high-symmetry reference frames within each rotation cycle, and aligns frames across cycles to correct for variations in rotation speed. This ensures that equivalent azimuthal positions are compared consistently when building per-angle timeseries.

Stage 2: Pattern Extraction

Diffraction features are segmented from each frame using deep learning models that separately identify streaks and spots. For each extracted feature, morphological metrics are measured, including FWHM, eccentricity, area, centroid position, and position relative to the specular spot.

Stage 3: Timeseries Analysis

For video data, the pipeline tracks how extracted metrics evolve across frames. For rotating data, frames are grouped by azimuthal angle so each metric is tracked per orientation. For stationary data, frames are sampled at regular intervals.Computed metrics: strain (relative change in feature spacing), lattice spacing (converted from reciprocal-space measurements), intensity (specular, half-order, and first-order reflections), FWHM, oscillation period, spot count, and per-feature shape properties.

Transition Detection

Automatic detection must be enabled for your deployment. If it is not enabled, new uploads and streams do not generate detections. See Changepoint Detection for availability and display controls. This section describes behavior where enabled.

The pipeline flags a changepoint when the detected surface reconstruction changes, for example from 2x1 to 4x1, or between 2x1 and no detected reconstruction. Changepoints appear as shaded bands on the growth analysis chart, colored by severity: High, Moderate, or Low.Reconstruction changes are flagged as Moderate, but the chart shows only High changepoints by default. To show other severities, click the gear icon (Chart settings) next to Growth Analysis, then turn on Moderate or Low under Changepoints.

Streaming Pipeline

For real-time streaming, the pipeline operates incrementally. Only new frames are processed and appended to existing timeseries rather than recomputed from scratch.

Investigate an Unexpected Change

Investigate an event in a notebook and examine the evidence.

Investigate Consistency Within a Growth

Analyze RHEED data consistency across a growth.

Platform

Get Started

Guides

Characterization

Reference

Overview

Key Metrics

Adding RHEED Data

Browser screen capture

Viewing Results

Azimuth Calibration

Reanalysis

Comparing Patterns

Analysis Pipeline

Stage 1: Data Cleaning and Standardization

Stage 2: Pattern Extraction

Stage 3: Timeseries Analysis

Transition Detection

Streaming Pipeline

Investigate an Unexpected Change

Investigate Consistency Within a Growth

​Overview

​Key Metrics

​Adding RHEED Data

​Browser screen capture

​Viewing Results

​Azimuth Calibration

​Reanalysis

​Comparing Patterns

​Analysis Pipeline

​Stage 1: Data Cleaning and Standardization

​Stage 2: Pattern Extraction

​Stage 3: Timeseries Analysis

​Transition Detection

​Streaming Pipeline

​Related Documentation

Investigate an Unexpected Change

Investigate Consistency Within a Growth

Overview

Key Metrics

Adding RHEED Data

Browser screen capture

Viewing Results

Azimuth Calibration

Reanalysis

Comparing Patterns

Analysis Pipeline

Stage 1: Data Cleaning and Standardization

Stage 2: Pattern Extraction

Stage 3: Timeseries Analysis

Transition Detection

Streaming Pipeline

Related Documentation