Atomize


Atomize is a modular software designed to control a wide range of scientific and industrial instruments, integrate them into a unified multifunctional setup, and automate routine experimental work. The general idea is close to FSC2 software developed by Jens Thomas Törring. Remote control of spectrometers is usually carried out using home-written programs, which are often restricted to doing a certain experiment with a specific set of devices. In contrast, the programs like FSC2 and Atomize are much more flexible, since they are based on a modular approach for communication with instruments and scripting language (EDL in FSC2; Python in Atomize) for data measuring.

Atomize1 uses liveplot library based on pyqtgraph as a main graphics library. Liveplot was originally developed by Phil Reinhold. Since then, several improvements have been made to use it in Atomize, and it has been directly embedded into Atomize.

Python Programming Language is used inside experimental scripts, which opens up almost unlimited possibilities for raw experimental data treatment. In addition, with PyQt, one can create experimental scripts with a simple graphical interface, allowing users not familiar with Python to use it. Several examples of scripts (with dummy data) are provided in /atomize/tests/ directory, including a GUI script with extended comments inside. Also a variant of the Atomize with GUI Control Window extension can be found here.

Currently there are more than 200 instrument specific and general functions available for over 27 different devices, including 6 series of devices. If you would like to write a module for the instrument that is not currently available, please, read this instruction.

Status


At the moment, Atomize has been tested and is currently used for controlling several EPR spectrometers using a broad range of different devices. The program has been tested on Ubuntu 18.04 LTS, 20.04 LTS, and 22.04 LTS.

General Structure


The general structure of Atomize can be visualized by the following figure:
Figure_1

More details


More details are provided in the JORS paper. Please cite it, if you use Atomize: 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, Vol. 13, Issue 1, Article 26. DOI: https://doi.org/10.5334/jors.594

  1. Atomize = A + TOM + ize; A stands for Anatoly, main developer; TOMo stands for the International TOMography center, our organization ↩