SegSpy

SegSpy is a headless, backend-pluggable segmentation library for electron-microscopy images in the HyperSpy ecosystem. It turns a Signal2D into a list of particle objects with calibrated morphology metrics — microscope-generic (TEM/SEM) and particle-type-agnostic.

Features

• Pluggable backends — swap segmentation algorithms behind one registry: traditional_cv (CLAHE → black-hat → threshold → morphology → GrabCut) and sam (Meta SAM Auto-Mask Generator with a 5-stage post-filter).

• Calibration-aware — reads HyperSpy axis scales, so lengths come out in nanometres.

• Generic morphology — area, equivalent diameter, Feret diameters, perimeter, aspect ratio, convexity, roundness, solidity, centroid — no domain-specific assumptions.

• Headless — a clean Python API and a SegSpy run CLI; no GUI required.

Quick navigation

• User guide
  • Installation
  • Quickstart
  • Configuration
  • Command-line interface
• Tutorials
  • Tutorial: segment a DM4 image
• Architecture overview
• API reference
  • Configuration
  • Data model
  • I/O helpers
  • Morphology
  • Backends
• Contributing
  • Development setup
  • Tests and linting
  • Pull requests
  • Reporting issues