Technical NoteA new Fiji-plugin for visualizing intra-annual density fluctuations and analyzing intra-annual theoretical volumetric flow rate fluctuations along wood cross-sections

•We present a plugin for Fiji to visualize and analyze intra-annual xylem features.•We propose intra-annual fluctuation analysis by theoretical volumetric flow rate.•We suggest a new pixel-column based parameter for intra-annual analysis.

Intra-annual analysis of wood samples by examination of xylem structure offers the possibility to reveal structural adaptations in the xylem of trees to varying climatic conditions with a high temporal resolution. Additionally, it can help closing the gap between annual tree ring width measurements and ecophysiological field studies.Typically, two approaches for intra-annual wood analyses are used: densitometry (x-ray or high frequency measurements) and analyses of microscopic images of cross-sections. While densitometry has recently become the most commonly used method, it requires expensive measurement devices, which are not necessarily part of standard laboratory equipment and accordingly not affordable for a significant number of researchers.We therefore present a new plugin for visualizing intra-annual density fluctuations (IADF) and, more specifically, for analyzing the theoretical volumetric flow rate with an adapted Hagen-Poiseuille law for elliptic conduits per pixel-column. The implemented algorithm represents an alternative for intra-annual analysis of microscopic cross-section images. The plugin has been developed for Fiji, a common package based on the open-source image processing program ImageJ to avoid the use of commercial programs for anatomical analyses.