SEEG electrode reconstruction and 3D neuroimaging visualization

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NeuXelec is a standalone desktop application for researchers working with stereoelectroencephalography (SEEG). It covers the full post-implantation workflow, from MRI/CT coregistration to electrode reconstruction, oblique reslicing, parcellation and 3D visualization, including MNI-space group analysis, without requiring any programming knowledge.

Research use only. NeuXelec is not a certified medical device and must not be used as the sole basis for any clinical, diagnostic, or treatment decision.

Website and documentation: https://neuxelec.com

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Workflow

1. Import & Coregistration - align MRI, CT, PET and SPECT into a shared space (ANTs rigid registration), automatic brain masking, SISCOM.
2. Electrode Reconstruction - two clicks per electrode on the CT; automatic contact localization in millimetre coordinates.
3. Oblique & Parcellation - reslice along each electrode axis, blend modalities, map every contact to its anatomical region.
4. 3D View & Export - render electrodes on the cortical surface, normalize to MNI152, export BIDS-compatible coordinates and publication figures.

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Installation

Option A - Windows installer (end users)

Download the latest installer from https://neuxelec.com/download and run it. No Python or dependencies required.

Option B - From source (developers)

Requires Python 3.10+ on Windows.

git clone <repository-url> NeuXelec
cd NeuXelec
python -m venv .venv
.venv\Scripts\activate
pip install -r requirements.txt
python scripts/run_neuxelec.py

External data not tracked in git (see .gitignore) and required at runtime:

• tools/ants/ - ANTs executables (coregistration, MNI normalization).
• templates/ - MNI152 template, brain mask and parcellation atlases.

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Project structure

src/neuxelec/
├── app.py                 # entry point: QApplication, logging, project loop
├── main_window.py         # main window, page lifecycle, safe teardown
├── state.py               # AppState - single source of truth
├── project_io.py          # project (.json) save / load, schema versioning
├── logging_config.py      # rotating file logging
├── coregistration.py      # ANTs coregistration wrappers
├── siscom.py              # SISCOM computation
├── controllers/           # interaction controllers (electrodes, menu)
├── pages/                 # the four workflow pages (files, recon, oblique, 3D)
├── ui/                    # dialogs and reusable widgets
├── workers/               # QThread workers for long-running tasks
└── utils/                 # imaging, coordinates, conversions, resources
resources/                 # Qt .ui files and images (icons, logo)
scripts/run_neuxelec.py    # dev launcher
tests/                     # pytest test suite

See ARCHITECTURE.md for the design and data flow.

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Development

pip install -r requirements.txt -r requirements-dev.txt

pytest                 # run the test suite
ruff check src tests   # lint
black src tests        # format
mypy                   # static type checking

See CONTRIBUTING.md for conventions.

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Building the executable

pyinstaller NeuXelec_windows.spec --clean --noconfirm
"C:\Program Files (x86)\Inno Setup 6\ISCC.exe" NeuXelec_setup.iss

This produces installer/NeuXelec_Setup_<version>.exe.

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License

Released under the GNU General Public License v3.0 (GPL-3.0). You are free to use, study, modify and redistribute NeuXelec, provided that any distributed derivative work is also released under GPL-3.0 with its complete source code made available. See LICENSE for the full text.

Research use only. NeuXelec is not a certified medical device and must not be used as the sole basis for any clinical, diagnostic or treatment decision.

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Citation

If you use NeuXelec in your research, please cite:

@software{veber2026neuxelec,
  author      = {Veber, Jules},
  title       = {NeuXelec: an all-in-one application for stereo-EEG electrode reconstruction and multimodal brain visualization},
  year        = {2026},
  url         = {https://neuxelec.com},
  institution = {HUG Geneva, University of Geneva}
}

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Acknowledgements

NeuXelec builds on Voxeloc (Monney et al., 2024), a MATLAB tool for SEEG electrode localization developed in the Human Neuron Lab. NeuXelec reimplements its two-point localization approach as a standalone Python application and extends it across the full SEEG workflow (coregistration, SISCOM, oblique reslicing, parcellation, MNI normalization and 3D visualization).

Monney J, Dallaire SE, Stoutah L, Fanda L, Mégevand P. Voxeloc: A time-saving graphical user interface for localizing and visualizing stereo-EEG electrodes. Journal of Neuroscience Methods. 2024;407:110154. doi:10.1016/j.jneumeth.2024.110154

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Author

Jules Veber · Hôpitaux Universitaires de Genève (HUG) and the Human Neuron Lab (HNL), University of Geneva · contact@neuxelec.com