pyccapt 0.2.0

A Python package for atom probe control and data calibration.

PyCCAPT

PyCCAPT is a modular, FAIR-oriented Python package for atom probe tomography (APT) instrument control, data calibration, and reconstruction workflows.

It provides:

• experiment control and acquisition for APT hardware
• calibration workflows such as t0 and flight-path estimation, ROI selection, voltage and bowl correction, and ranging
• reconstruction and visualization tooling
• interoperable data export for HDF5-based workflows and common APT exchange formats

Project Scope

PyCCAPT was developed and validated on the OXCART atom probe platform and is designed to be adaptable to other APT systems through device-specific modules. Current integrations include detector backends such as Surface Concept and RoentDek, together with modular support for common laboratory hardware.

Installation

PyCCAPT requires Python >=3.9.

Recommended Quick Start (Conda)

For most users, this is the best way to install PyCCAPT:

conda create -n pyccapt python=3.11
conda activate pyccapt
python -m pip install --upgrade pip
pip install "pyccapt[full]"

If you want to work from this repository instead of PyPI:

git clone https://github.com/mmonajem/pyccapt.git
cd pyccapt
conda activate pyccapt
pip install -e ".[full]"

Predefined conda environment files are also included in the repo:

conda env create -f environment.yml
conda env create -f environment.full.yml

Other Installation Options

1. Install from PyPI:

pip install pyccapt

Optional dependency groups:

pip install "pyccapt[calibration]"
pip install "pyccapt[control]"
pip install "pyccapt[full]"

Module-specific editable installs:

pip install -e ".[control]"
pip install -e ".[calibration]"

Running PyCCAPT

Start the control application:

pyccapt

Fallback entrypoint:

python -m pyccapt.control

Run tests:

pytest -q --run-calibration
pytest -q --run-control
pytest -q

Run calibration tutorials:

jupyter lab

Then open notebooks under pyccapt/calibration/tutorials.

Configuration

Control runtime configuration is stored in pyccapt/config.toml.

Control GUI electrode labels are stored in pyccapt/control/electrode.toml:

[electrodes]
names = [
  "NiC1", # Nickel electrode
  "CuC1", # Copper electrode
]

For device toggles, prefer enabled and disabled. Legacy on and off values still work.

Control Highlights

The control stack includes the main acquisition GUI together with dedicated windows for gates, pumps and vacuum, cameras, laser, stage control, visualization, and baking. Startup reports unavailable configured ports clearly, GUI error boxes wrap long messages, and Access Override now asks for confirmation before allowing a run to proceed with missing enabled devices.

Vacuum logs are written under pyccapt/files/logs/vacuum, and baking logs are written under pyccapt/files/logs/baking/<timestamp>.

Calibration Highlights

PyCCAPT calibration workflows cover detector hit maps, FDM views, mass-spectrum calibration, bowl and voltage correction, reconstruction, and downstream visualization.

Processed calibration datasets can be exported as HDF5, EPOS, POS, and ATO.

The visualization helpers also include optional two-segment precipitate clustering with a Min-Max algorithm so a selected precipitate population can be segmented directly in the 3D and iso-surface views.

For control part of the package you can follow the steps on documentation.

Documentation

• Full documentation: Read the Docs
• Control guide: docs/configuration
• Calibration tutorials: docs/tutorials

Google Colab notebooks:

• Data processing
• Visualization
• t0 and flight path estimation

Data Structures

• Control data model: pyccapt/control/DATA_STRUCTURE.md
• Calibration data model: pyccapt/calibration/DATA_STRUCTURE.md

Tutorial Dataset

Calibration tutorial data (pure aluminum), including raw and processed outputs, is available on Zenodo:

Citation

If you use PyCCAPT in your work, please cite:

@article{monajem2025pyccapt,
  title={PyCCAPT: A Python Package for Open-Source Atom Probe Instrument Control and Data Calibration},
  author={Monajem, Mehrpad and Ott, Benedict and Heimerl, Jonas and Meier, Stefan and Hommelhoff, Peter and Felfer, Peter},
  journal={Microscopy Research and Technique},
  volume={88},
  number={12},
  pages={3199--3210},
  year={2025},
  publisher={Wiley Online Library}
}

Citation metadata is also available in CITATION.cff.

Contributing

Contributions are welcome. See CONTRIBUTING.md for development workflow and pull-request guidance.

Support

• Issues and bug reports: GitHub Issues
• Contact: Mehrpad Monajem ([e-mail])

License

PyCCAPT is licensed under the GNU General Public License v3.0. See LICENSE.