1D Spectroscopy

Navigate a map of per-pixel spectra and watch the spectrum change live under the crosshair — the basic EELS/EDS spectrum-imaging workflow.

Follow along in the app

Every step below is also a live walkthrough inside SpyDE: Help → 1D Spectroscopy → Guided tour. The tour loads the same small tutorial dataset for you (no download), highlights each control as you go, and closes the example data again when you exit.

Steps

1. What you’ll do

Spectroscopy data (EELS, EDS) pairs a spectrum — intensity per energy channel — with every position in a scan. SpyDE shows the same navigator + linked-signal layout as imaging data, except the signal window is a 1D spectrum plot instead of a 2D pattern.

Tip

A small tutorial map (Tutorial Data → Spectroscopy, two Gaussian peaks whose position/width vary per pixel) is loaded for you — no download needed.

2. Navigator + spectrum window

The navigator (left) shows the 32×32 scan grid; the signal window (right) plots the spectrum — intensity vs. channel — at the crosshair position.

3. Move the crosshair, watch the spectrum change

Drag the crosshair across the navigator — the two peaks in the spectrum window shift and change height as you cross the map, since each pixel carries its own peak position and width.

4. The plot toolbar

Hover the spectrum window to reveal its floating toolbar — Zoom, Reset, and Add Selector (to place an integration region) work the same way here as on any 2D plot.

5. Reading the axes

The Plot Control dock shows the spectrum’s channel axis and intensity scale for the active window — the same dock used for every plot in SpyDE.

More information

A spectrum image stores a full spectrum — EELS or EDS — at every position of a scan. The data has the same navigator/signal shape as 4D-STEM, only the signal is one-dimensional: navigating the map plays the spectrum back position by position, and integrating a real-space region averages spectra to trade spatial resolution for signal-to-noise.

The usual analysis is quantitative rather than visual: subtract a background (a power law before an EELS edge, a bremsstrahlung model under EDS lines), fit a model of components to the remaining signal, and map a fitted parameter — an edge intensity, a peak position, a composition — back over the scan.

Tip

SpyDE reads and displays this data through HyperSpy; the quantitative EELS/EDS methods live in eXSpy, HyperSpy’s spectroscopy extension.

Further reading

SpyDE wraps pyxem, HyperSpy, eXSpy, kikuchipy and orix; those projects document the underlying methods in far more depth than a walkthrough can.

• eXSpy — EELS user guide

  Thickness, zero-loss alignment, deconvolution, Kramers-Kronig analysis and EELS curve fitting.

• eXSpy — EDS user guide

  Background subtraction, line fitting and quantification for energy-dispersive X-ray data.

• eXSpy — EELS curve fitting example

  A complete worked example: load, set microscope parameters, build a model, fit, plot.

• HyperSpy — Signal1D tools

  Background removal, smoothing, peak finding and spectrum alignment.

• HyperSpy — Model fitting

  Components, fitting strategies and fitting a model across a whole spectrum image.