JFGui — Control Interface for the JUNGFRAU Detector on JEOL TEM

JFGui is a graphical user interface for operating the JUNGFRAU hybrid pixel detector integrated with JEOL transmission electron microscopes (TEM). It streamlines detector configuration, acquisition, and live visualization for electron diffraction workflows.

Full documentation: https://epoc-ed.github.io/manual/

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Table of Contents

• Features
• Installation (Conda + local recipe)
• Startup
• Configuration
• Troubleshooting
• Development
• License
• Authors & Acknowledgments
• References / Cite Us

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Features

• Control of JUNGFRAU detector parameters, trigger modes, and frame acquisition.
• Integration with JEOL TEM workflows.
• Live preview and basic visualization of frames.
• Written in Python with a Qt (PySide6) frontend.
• Reproducible builds using a Conda recipe.

For detailed user and operator guides, see the manual: https://epoc-ed.github.io/manual/

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Installation (Conda + local recipe)

Below is a condensed “How-To” for building and installing JFGui as a Conda package from a local recipe. For the canonical version, refer to the manual page.

A) Create the environment

git clone git@github.com:epoc-ed/GUI.git
cd GUI
conda create --name jf_gui python=3.10
conda activate jf_gui
cd jungfrau_gui
pip install -r requirements.txt

B) Build and install as a Conda package

my_project/
├─ jungfrau_gui/
├─ setup.py
├─ MANIFEST.in
└─ conda-recepie/
   └─ meta.yaml

conda install conda-build     # if not already installed
conda build conda-recepie     # produces a .conda/.tar.bz2 in conda-bld/<platform>
conda install --use-local jungfrau_gui \
  || conda install /path/to/conda-bld/noarch/jungfrau_gui-YYYY.MM.DD-py_0.conda

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Startup

This is a brief field guide. For the complete startup flow and screenshots, see the Start up section of the manual.

1) TEM‑PC — Relay server (Windows, PyJEM)

• Goal: Allow microscope control from other machines via a ZMQ socket.
• Usual case: It may already be running.

Check & start

1. On the TEM-PC, verify if server_tem.py is running (Miniconda PowerShell Prompt).
   • If running, continue to CameraPC below.
2. If not running, double‑click: C:\Users\JEM User\Documents\DataExchange\bat\run_tem_server.bat

Manual fallback (if the .bat fails)

# Open: Miniconda PowerShell Prompt (Anaconda submenu)
# Disable Quick Edit Mode in the console properties if scripts get interrupted.

cd C:\ProgramData\EPOC
conda activate vjem38  # conda environment on TEM-PC with PyJem 3.8 installed
python server_tem.py

2) CameraPC — Backend & GUI

• As of 2025‑01‑24, Jungfraujoch broker and writer are auto‑started at boot on noether.
• Future releases will use systemd services; keep an eye on the manual for updates.

Sanity checks on DAQ server (optional)

ssh noether
ps -elf | grep writer     # expect jfjoch_writer ... tcp://localhost:5500
ps -elf | grep broker     # expect jfjoch_broker /opt/config/broker_jf1M.json

# Metadata updater
ps -elf | grep metadata_update_server
# If missing or stuck:
python -i /data/epoc/storage/jem2100plus/metadata_update_server.py
# If looping in error: ctrl+z; kill %1; fg; re-run the command above.

Initialize detector & launch GUI

1. Open the web UI: http://noether:5232/
2. Click INITIALIZE in the webpage.
3. Launch the desktop GUI:

conda activate jf_gui
# Run the JFGui
# Option 1:
jungfrau_gui            # command after local build
# Option 2:
python launch_gui.py    # without local build from the /GUI folder

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Configuration

• Detector host/port: Set the control server/IP and ports matching your JUNGFRAU readout system.
• Acquisition settings: Number of frames, integration time, trigger mode, gain mode.
• Data paths: Output directories for saved data and logs.
• JEOL integration: Ensure microscope-side services/permissions match your site deployment.

For setting up the Jungfraujoch backend, consult the Jungfraujoch section in the manual: https://epoc-ed.github.io/manual/

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Troubleshooting

• Package not found after build
  Use direct installation from the built .conda/.tar.bz2 path (see above).

• Missing Qt plugins / blank window
  Verify that PySide6 (or Qt) is installed cleanly in the jf_gui environment.

• Cannot connect to detector
  Check network routes, firewall rules, and that the readout/DAQ service is running and reachable.

• Unknown module errors
  Re-run:

  pip install -r jungfrau_gui/requirements.txt

For more, see the manual: https://epoc-ed.github.io/manual/.

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Development

Install in editable mode

conda activate jf_gui
pip install -e .

Contributing

• Fork the repository, create a feature branch, and submit a PR.
• For larger changes, open an issue first to discuss design and scope.
• Please include concise descriptions, reproducible steps, and screenshots when relevant.

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License

This project is distributed under the MIT License. See the LICENSE file for the full text.

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Authors & Acknowledgments

Core contributors

• Khalil Ferjaoui — PSI
• Kiyofumi Takaba — University of Vienna
• Erik Fröjd — PSI
• Tim Gruene — University of Vienna

Acknowledgments
We thank the Paul Scherrer Institute (PSI), the University of Vienna, and the broader EPOC Electron Diffraction community for support, feedback, and testing during integration on JEOL instruments.

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References / Cite Us

Please cite the following when using JFGui and related JUNGFRAU-based measurements in your work.

• Ferjaoui, K., et al. A 1 Megapixel charge integrating hybrid pixel detector for electron diffraction. JINST (2025).

BibTeX (template)

@article{Ferjaoui2025JINST,
  author  = {Ferjaoui, K. and others},
  title   = {A 1 Megapixel charge integrating hybrid pixel detector for electron diffraction},
  doi = {10.1088/1748-0221/20/12/C12007},
  journal = {Journal of Instrumentation},
  title = {A 1 Megapixel charge integrating hybrid pixel detector for electron diffraction},
  issue = {12},
  volume = {20},
  pages = {C12007},
  url = {https://iopscience.iop.org/article/10.1088/1748-0221/20/12/C12007},
  year = {2025}
}