Atomize is a modular software for controlling scientific and industrial instruments, combining them into a unified multifunctional setup, and automating routine experimental work. Experiments are ordinary Python scripts: they import an instrument module, call its functions, and push the data to a live plot.
The idea follows FSC2 by Jens Thomas Törring. Home-written control programs are usually locked to one experiment and one set of devices. Atomize and FSC2 separate the two: instrument communication lives in modules, and the experiment lives in a script (EDL in FSC2, Python in Atomize).
- 55+ instruments across 19 categories: oscilloscopes, digitizers, AWGs, pulse programmers, lock-ins, temperature and field controllers, microwave bridges, and more. See the full list.
- Python scripting with NumPy on hand for raw-data treatment; PyQt is available for scripts that need their own small GUI.
- Live plotting built on liveplot by Phil Reinhold, embedded and extended on top of pyqtgraph: 1D and 2D plots, cross-sections, cursors, fitting.
- Math modules for fitting, FFT and phase correction, and signal processing.
- Test mode runs any script end to end without hardware, validating the arguments on the way.
- Extendable. A new instrument is one module plus one config file; see writing modules.
An extended variant with a GUI control window for a pulsed EPR endstation lives in Atomize_ITC.
pip install atomize-py
atomizeOptional extras:
| Extra | Installs | Needed for |
|---|---|---|
serial |
pyserial | RS-232 instruments |
modbus |
minimalmodbus | Modbus instruments |
math |
SciPy | math modules |
bots |
pyTelegramBotAPI | Telegram notifications |
test |
pytest | the test suite |
pip install "atomize-py[serial,modbus,math]"Some instruments also need a vendor driver: linux-gpib for GPIB, SpinAPI for Pulse Blaster ESR 500 Pro, Spcm for Spectrum M4I cards. Full details are in the requirements.
Atomize needs Python 3.10 or newer. It is used daily on several EPR spectrometers and has been tested on Ubuntu 18.04, 20.04 and 22.04 and on Windows 10.
On start, Atomize prints where its files are:
SYSTEM: Linux
DATA DIRECTORY: /path/to/experimental/data/
SCRIPTS DIRECTORY: /path/to/scripts/
MAIN CONFIG PATH: ~/.config/atomize-py/main_config.ini
DEVICE CONFIG DIRECTORY: ~/.config/atomize-py/device_config/
EDITOR: nano
Edit main_config.ini to set the text editor, the default data and script directories, and the Telegram bot credentials:
[DEFAULT]
editor = subl # Linux
editorW = C:\path\to\editor.exe # Windows
open_dir = /path/to/experimental/data/
script_dir = /path/to/scripts/
telegram_bot_token =
message_id =Each instrument has its own config file in the device config directory. Pick the protocol (GPIB, RS-232, Ethernet, Modbus) and fill in the address and settings of your device, as described in protocol settings.
Import a module, create its class (always named after the module file), and call its functions. Creating the class connects to the instrument.
import numpy as np
import atomize.device_modules.Keysight_3000_Xseries as keys
import atomize.device_modules.Lakeshore_331 as tc
import atomize.general_modules.general_functions as general
import atomize.general_modules.csv_opener_saver as openfile
scope = keys.Keysight_3000_Xseries()
lakeshore = tc.Lakeshore_331()
file_handler = openfile.Saver_Opener()
general.message(scope.oscilloscope_name())
temperature = lakeshore.tc_temperature('A')
y = scope.oscilloscope_get_curve('CH1')
x = np.arange(len(y))
general.plot_1d('Trace', x, y, xname = 'Point', yname = 'Signal', yscale = 'V')
file_handler.save_data('trace.csv', np.c_[x, y], header = f'T = {temperature} K')More examples with dummy data, including a script with its own GUI, are in atomize/script_examples/. The usage guide covers the main window, live plotting, test mode, and data files.
If you use Atomize, please cite the JORS paper:
Melnikov A., Vedkal A., Ishchenko A., Veber S. Atomize: A Modular Software for Control and Automation of Scientific and Industrial Instruments. Journal of Open Research Software, 13(1), 26 (2025). DOI: 10.5334/jors.594
The current interface shown with synthetic demonstration data.
