columx 2.3.0

Advanced electron optics simulation platform for TEM/STEM/SEM column design

ColumX

Advanced Electron Optics Simulation Platform for TEM/STEM/SEM Column Design

ColumX is a comprehensive Python library for electron optics simulation, covering paraxial ray tracing, aberration calculation, wave optics, multislice propagation, crystal potentials, and full TEM/STEM column modeling. It is designed for researchers and engineers working on electron microscope column design, beam physics analysis, and image simulation.

Features

ColumX provides 20 physics modules organized into four layers:

Ray Optics — paraxial, ray3d, glaser, aberration, electrostatic_paraxial Magnetic and electrostatic lens modeling with Glaser analytical fields, adaptive-power Seidel aberration integrals (Cs < 0.04%, Cc < 0.02% vs MEBS), 5th-order aberration framework (C5, S5, Krivanek naming), and 3D relativistic Lorentz ray tracing.

Wave Optics — wave, multislice, crystal Contrast transfer function with spatial/temporal coherence envelopes, STEM probe formation, FFT-based multislice propagation engine, and crystal structure module with Kirkland scattering factors for 7 built-in crystal presets (Si, Ge, GaAs, SiC, MgO, Al, Au).

Advanced Imaging — stem, cbed, eels, hrtem, dpc STEM imaging chain (probe, annular detectors BF/ADF/HAADF, Z-contrast), convergent beam electron diffraction with HOLZ lines, EELS spectrum simulation with thickness measurement, HRTEM imaging (WPOA linear and multislice nonlinear), and differential phase contrast with electric/magnetic field reconstruction.

Column & Infrastructure — column, lens_cascade, multipole, source, deflection, coulomb, fem2d, field, instruments, constants Full TEM column simulator, multi-lens cascade with Conrady aberration propagation, multipole elements, electron gun models (thermionic/field emission/Schottky), scanning deflection, space charge and Boersch effect, 2D FEM field solver, and instrument presets (Titan, Themis, ARM200F, ARM300F2).

Installation

# Core library
pip install columx

# With GUI (PySide6)
pip install "columx[gui]"

# With web API (FastAPI)
pip install "columx[api]"

# Everything
pip install "columx[all]"

From Source

git clone https://github.com/allen-li1231/ColumX.git
cd ColumX
pip install -e ".[all]"

Quick Start

Glaser Lens

from columx import GlaserLens

lens = GlaserLens(V=200e3, B0=0.5, a=3e-3, z0=-30e-3, zf=60e-3)
print(f"Focal length: {lens.analytical_efl()*1e3:.2f} mm")
print(f"Magnification: {lens.analytical_magnification():.3f}")
print(lens.summary())

CTF and Probe

from columx import ContrastTransferFunction, STEMProbe

ctf = ContrastTransferFunction(V=200e3, Cs=1.2e-3, Cc=1.2e-3, defocus=-50e-9)
print(f"Scherzer resolution: {ctf.scherzer_resolution()*1e10:.2f} A")

probe = STEMProbe(V=200e3, Cs=1e-3, alpha=10e-3)
print(f"Probe FWHM: {probe.probe_size()*1e10:.2f} A")

Multislice Simulation

from columx import MultisliceEngine
from columx.multislice import phase_grating_potential
import numpy as np

V = np.stack([phase_grating_potential(
    nx=128, ny=128, Lx=5e-9, Ly=5e-9,
    period=1e-9, amplitude=10.0
)] * 20)

engine = MultisliceEngine(V=200e3, nx=128, ny=128, Lx=5e-9, Ly=5e-9, dz=0.5e-9)
psi_exit = engine.run(V)
dp = engine.diffraction_pattern(psi_exit)

Crystal Potential

from columx import CrystalStructure, projected_potential

si = CrystalStructure.from_preset("Si")
V_proj, info = projected_potential(si, nx=256)
print(f"MIP: {info['MIP_V']:.1f} V")

Web API

Start the REST API server:

python run_web.py
# → http://127.0.0.1:8000 (interactive frontend)
# → http://127.0.0.1:8000/docs (OpenAPI documentation)

Endpoints: POST /api/glaser/compute, POST /api/wave/ctf, POST /api/wave/probe, POST /api/multislice/simulate, POST /api/crystal/potential, POST /api/stem/probe.

Desktop GUI

Launch the PySide6 desktop application with 20 interactive panels:

python gui/columx_gui.py

Testing

cd tests
python test_all.py        # Core modules (13 modules)
python test_new_physics.py # v2.0+ modules
python test_crystal_stem.py # Crystal + STEM + CBED + EELS + HRTEM + DPC

269 tests covering all 20 modules.

Architecture

columx/
├── columx/           # 20 physics modules (13,000+ lines)
├── api/              # FastAPI REST API layer
├── web/              # Vue3 + Plotly.js frontend
├── gui/              # PySide6 desktop GUI (20 panels)
├── tests/            # 269 tests across 8 test files
└── docs/             # Architecture documentation

Validation

ColumX has been systematically validated against MEBS (Munro's Electron Beam Software):

• Paraxial: M and theta accuracy 0.006%
• Aberrations: Cs < 0.04%, Cc < 0.02% (200 kV, objective lens)
• 5th order: C5 verified against Krivanek analytical values
• MEBS compatibility: match_mebs=True mode replicates MEBS mixed relativistic convention

References

1. Glaser, W. Grundlagen der Elektronenoptik (Springer, 1952)
2. Hawkes, P.W. & Kasper, E. Principles of Electron Optics (Academic Press, 1989)
3. Reimer, L. Transmission Electron Microscopy 5th ed. (Springer, 2013)
4. Krivanek, O.L. et al. Ultramicroscopy 110 (2010) 571-585
5. Kirkland, E.J. Advanced Computing in Electron Microscopy 2nd ed. (Springer, 2010)

License

MIT License. See LICENSE.