First Steps#

A quick orientation to SpyDE: the navigator and signal windows, the linked crosshair, per-window toolbars, and the Plot Control dock.

Follow along in the app

Every step below is also a live walkthrough inside SpyDE: Help → First Steps → 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. Welcome to SpyDE#

SpyDE visualizes and analyzes electron microscopy data — TEM, STEM, Cryo EM, 4D-STEM, EELS. You work with windows: a navigator shows the scan, a signal window shows the pattern or spectrum at the crosshair, and toolbars on each window run analyses.

Tip

A small tutorial scan (Tutorial Data → Navigation & Virtual Imaging) is loaded for you — no download needed.

2. Two linked windows#

The navigator (left) shows the scan grid with a crosshair; the signal window (right) shows the diffraction pattern at that crosshair position. Every dataset you open works this way.

3. Move the crosshair#

Drag the crosshair on the navigator — the signal window updates live to show the pattern at the new scan position. Try it now.

4. Hover a window for its toolbar#

Hover any window to reveal its floating toolbar — the tools that act on that window (Find Vectors, Virtual Imaging, FFT, and more all live here, depending on the data).

5. The Plot Control dock#

The dock on the right shows the contrast histogram, axes, signal-tree, and metadata for whichever window is active — your control panel for the current plot.

6. Where to go next#

Ready for a real workflow? Open Help → Virtual Imaging or Help → Finding Diffraction Vectors for a guided walkthrough on its own tutorial dataset.

More information#

SpyDE is a desktop front end for the Python electron-microscopy stack: HyperSpy for the multidimensional signal model and lazy/out-of-core loading, pyxem for the 4D-STEM methods, orix for crystal orientations. Everything you do in the interface is a call into those libraries, so an analysis you build here has a direct equivalent in a notebook — and vice versa.

The navigator/signal window pair is HyperSpy’s own idea of navigation and signal axes made interactive, which is why the same layout appears whether the signal is a diffraction pattern, an image or a spectrum.

Tip

Pick a technique from the Help menu for a walkthrough of a specific workflow.

Further reading#

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