BioLink

BioLink — synchronized psycho-physiological and behavioural data acquisition (PLUX + stimulus events, e.g. from PsychoPy via serial).

User manual · LGPLv3

About

BioLink acquires physiological data from PLUX Biosignals devices and aligns stimulus/event markers (typically sent over a serial port from PsychoPy or similar) on a single timeline. Recordings are saved as .npz + .json and can be exported to tab-separated .txt.

Cross-platform desktop app: Windows, macOS, and Linux.

Requirements

• Python 3.10+
• Dependencies in requirements.txt (PySide6, numpy, matplotlib, pyserial)
• PLUX: OpenSignals with the Python plux module, or MAC address dummy for testing without hardware

Install & run

git clone git@github.com:hurxan/biolink-v2.git
cd biolink-v2
pip install -r requirements.txt
python -m biolink

• macOS / Linux: ./run.sh
• Windows: double-click start.bat or python -m biolink

Settings are stored in settings.json (project root). Logs go to log/.

PLUX hardware

1. Pair the device (USB dongle or Bluetooth, PIN often 123).
2. Install OpenSignals (r)evolution so the Python plux module is available.
3. If BioLink does not find it automatically, set BIOLINK_PLUX_PATH to the directory that contains plux (e.g. OpenSignals .../code/modules/WIN32 or MAC64).

Use find devices in the app or enter the MAC address manually. For offline development, set Plux MAC to dummy.

Extensions

Custom extensions live under biolink/extensions/<name>/. Included demos:

• template — minimal dialog + live samples (learning)
• marker_panel — manual/auto markers for testing without PsychoPy or serial

Extensions guide: docs/EXTENSIONS.md

Usage

See the complete user manual (installation, GUI, PLUX, serial/PsychoPy, data formats, troubleshooting).

Quick tips:

• Subject ID nolog: run without saving .npz/.json
• Serial events: lines terminated with \n; #END stops the session; #ID:… can supply Subject ID
• Tools → Convert log to txt / Plot BioLink Data

Built with

• Python 3, PySide6
• numpy, matplotlib, pyserial

Legacy (BioLink 1.x)

Documentation for the retired Python 2 / GTK application is archived separately:

• docs/legacy/ — index
• Manual.pdf — original 1.x user manual (reference; UI and install steps differ from BioLink 2)

Acknowledgments

• Original BioLink / BioLinkJ (University Hospital Zurich)
• Community forks and contributors