X-ray micro-CT pipeline for large-scale tree-ring densitometry studies

Tree-ring data provides essential insights into historical climate conditions and current ecosystem dynamics. Wood density measurements complement traditional tree-ring width series by extracting additional climatic information embedded within tree rings, with maximum latewood density serving as the gold standard for summer temperature reconstructions. However, the labor-intensive wood sample preparation required by conventional techniques is one of the main factors limiting the more widespread use of tree-ring densitometry. X-ray micro-computed tomography (X μ CT) offers a novel, non-destructive, 3D densitometry technique that enables the simultaneous study of tree-ring width and wood density at high resolution and with minimal sample preparation. Despite its potential, the lack of a streamlined and time-efficient X μ CT workflow has hindered its broader application in the past. Here we present a highly optimized X μ CT pipeline aimed at large-scale tree-ring densitometry studies, capable of processing large amounts of increment cores with a low demand for human labor time (2.2–5.4 min per 35 cm sample length). Key parts include large and efficient sample holders (16–48 samples per scan), optimized and standardized scan settings (helical X μ CT at 15, 30, and 60 μ m voxel size), and three custom software packages (facilitating scan processing, ring indication, and cross-dating). Overall, this X μ CT toolchain represents a significant leap forward in high-resolution tree-ring densitometry, enabling large-scale studies with a wide spatial extent, high replication, and/or long temporal range. • X-ray micro-CT pipeline enables large-scale tree-ring densitometry studies. • 3D-printed sample holders are designed for high-throughput scanning. • Standardized scan settings ensure quality and compatibility across studies. • Free software enables user-friendly scan processing and tree-ring indication.