Mapping Reciprocal Space to Real Space: A Semi-Automated Tool for Advanced Defect Analysis in 3D

Recent advances in self-assembly and microscopy allow for 3D imaging of complex nanostructures arising in both soft and hard condensed matter systems. At the same time, advances in computing allow for sophisticated simulation models that aid in the understanding and exploration of these systems. However, both experimental and computational analysis of complex crystals at the atomic, molecular and colloidal scales face a common challenge: the lack of generalizable tools for structure, strain, and dislocation analysis. Generalizable methods such as Fourier filtering often rely on manual inspection of structural data, making them impractical for systematic, large-scale studies. Although domain specific tools for automated analysis of 2D electron diffraction patterns exist, these tools are not generalizable to arbitrary 2D and 3D datasets. Here, we present a structure agonistic software tool for semi-automated analysis of 2D and 3D particle data. Our algorithm is robust to noise originating from liquid, polycrystalline or otherwise disordered regions, and can be used to analyze strain in atomic, molecular and colloidal crystals of varying complexity and from disparate data collection sources. This method holds promise for advancing structural studies across a variety of domains by providing researchers with a powerful, generalizable tool for understanding and exploring complex crystal structures.