The Pixel Anomaly Detection Tool: a user-friendly GUI for classifying detector frames using machine-learning approaches

J Appl Crystallogr. 2024 Feb 12;57(Pt 2):529-538. doi: 10.1107/S1600576724000116. eCollection 2024 Apr 1.

Abstract

Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy-to-use graphical user interface, specifically designed to support the detectors, file formats and software available at most X-ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X-ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data-analysis tasks such as hit finding during an experiment, without needing to write code.

Keywords: X-ray diffraction patterns; X-ray free electron lasers; data analysis; experimental artefacts; graphical user interfaces; image classification; machine learning; serial crystallography.

Grants and funding

This work was supported by the National Science Foundation by BioXFEL STC (award 1231306) and the Biodesign Center for Applied Structural Discovery at Arizona State University. We also acknowledge that the data presented in the test case made use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, which is supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences under contract No. DE-AC02-76SF00515.