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SIMPLE

SIMPLE is a high‑performance, end‑to‑end cryo‑EM image processing and reconstruction platform.

It transforms raw electron microscopy data --- movies, micrographs, and particle images --- into scientifically meaningful outputs including:

  • 2D class averages
  • High-resolution 3D reconstructions
  • Symmetry analysis
  • Atomic-level structural models

SIMPLE supports interactive batch workflows and fully automated streaming pipelines, scaling seamlessly from single workstations to distributed HPC environments.

Features

  • End-to-end cryo‑EM workflow
  • Streaming data processing
  • HPC scalability
  • Modular architecture
  • Test-driven development
  • Production-ready scientific computing environment

Start Here

  • Installation — covers requirements, standard builds, custom install paths, updates, and the NICE GUI build.
  • Tutorials — points to the existing workflow guide for moving from raw movies to ab initio 3D reconstruction.
  • Code Overview — maps the main source tree and important subsystems.
  • Developer Docs — collects onboarding and design notes for contributors.

License

SIMPLE is distributed under the GNU General Public License v3 (GPLv3) or later.

This software is provided without warranty, including without implied warranty of merchantability or fitness for a particular purpose.

See the GNU General Public License for details.

Release Notes

This section indexes the existing release-note files.