Digital Imaging & Online Analyses of Tree Rings
EMERGING TECHNOLOGIES FOR DENDROCHRONOLOGY
Dendrochronology is an incredibly potent tool for environmental analysis. It is also being increasingly applied by researchers from a diverse set of educational backgrounds, most with limited resources.
With a focus on high throughput, low cost tree-ring data development and improved outcomes of data access, transparency and open science standards, we are developing novel capacity for ultra-high resolution imaging and dynamic online database handling of gigabyte-scale image files.
Leveraging various emerging technologies, our vision is to achieve high quality and ultra high resolution image archives to complement entire collections of physical specimens, and to develop open source, online tools for image analyses and curation. This collaborative project links the UMN GriffinLab & the CLA AISOS. For more information, or to become involved, please contact Daniel Griffin.
More information is below, and at https://dendro.elevator.umn.edu
ULTRA HIGH RESOLUTION PHOTOGRAPHY OF ENTIRE COLLECTIONS OF TREE-RING SPECIMENS
Motivated by the beauty and scientific value inherent to wood anatomy, and by the obstinate use of flatbed scanners to produce mediocre tree-ring images, we champion gigapixel macro photography as one straightforward and adaptable paradigm to elevate reflected light imaging standards in dendrochronology. Leveraging various emerging technologies, our vision is to achieve high quality and ultra high resolution image archives to complement entire collections of physical specimens.
Ultra high resolution imaging must be a priority for geochronology. Many labs use image analysis workflows, but standard practices in tree-ring research have languished around old technology. Scanners like the EpsonXL fail to resolve micro rings and the myriad anatomical structures of increasing scientific interest. We are setting a new standard with contemporary digital cameras, high magnification lenses, integration of techniques from panoramic and macro photography, and operational automation. The graphics below illustrate fundamental resolution limitations.
Our article on this topic appeared in Tree-Ring Research in July 2021.
DendroElevator is an open-source web platform for tree-ring image curation, visualization, and analysis. The system is optimized to maximize access to gigapixel images of tree rings and related paleoenvironmental proxy datatypes for remote research and distanced collaboration.
DendroElevator features a browser-based toolkit for tree-ring image visualization and time series measurement built for Elevator, a cloud-hosted digital asset management software with curation and robust streaming capabilities for file types of any size and common 2D and 3D formats, plus adaptability for various metadata and access permissions schemas.
DendroElevator constitutes an initial realization of our vision to create an open source, easily accessible online repository of high quality tree-ring imagery for entire collections of specimens. More information is here.
The image above illustrates the microscopic growth ring for 1580, and appeared in Science in April 2020. The tree ring core specimen comes from a big-cone Douglas-fir (Pseudotsuga macrocarpa) in southern California, and covers the years 1545–2016, CE. The full photo is 404,684 pixels wide by 6,092 pixels tall, with a resolution of 780 pixels per millimeter. The foundational .tiff file size is over 4 gigabytes.
GIGABYTE IMAGE HANDLING & WEB-BASED MICROMETRY
Panoramic macrophotography produces gigabyte-scale image files that bring most proprietary software packages to a grinding halt. Image file handling presents a substantial challenge and requires a new paradigm for data management and analyses. For image display and basic micrometry, we are developing open-source, web-browser based software solutions that are flexible and community driven. Tree-ring analysis workflow is our testbed, and we are partnering with other data development labs to maximize use across various proxies in geochronology. Check out the video here for a preview.
The April 2021 video below provides an overview of the project activities.