Tree Core Analysis with X-ray Computed Tomography

The scope of my research is to study wood growth and its response to climate. The questions I'm trying to answer is, how can we reconstruct the climate of the past, and what is the tree response to current climate change? So the current experimental challenges that we face are, among others, the large data volumes that we obtain with X-ray CT scanning.

So we need to find a proper balance between the number of samples that we want to scan and the required resolution. The X-ray CT techniques has allowed us to scan tree cores at an unprecedented rate. We have density profiles both from tropical and temperate regions.

So the main advantages that we have with our technique is that we can do a lot of high throughput scanning and analysis, but also that all the indications and manipulations that we do are traceable along the entire tool chain, including the tree ring indications. This tool will allow us to update current maximum latewood density chronologies, and also measure wood properties on tree cores from all over the world, especially in regions where there's little data available. To begin, core a tree using a Pressler borer.

Put the tree cores unglued into six-millimeter paper straws and mark the straws using a pencil. Fill the round-bottomed flask with solvent and place the straw onto a stainless steel support in the Soxhlet apparatus with a cooler on a laboratory heater. After siphoning, dry the cores for 24 hours in an oven at 103.5 degrees Celsius under exhaust ventilation.

The next day, perform a hot water Soxhlet extraction for 24 hours. Place the samples in the steel sample holders and dry them again for 24 hours. Then place the cores from the seal sample holder back in the straws.

To begin core scanning, depending on the research purpose, select the proper sample holder type, load the tree cores in paper straws into the sample holder, and record the position of each core in the downloadable spreadsheet template. Perform X-ray micro CT scanning following proper settings and scanning protocol. To obtain density values, install Core Processor, Ring Indicator, and Core Comparison toolboxes using the given link.

Next, for pre-processing the core volumes with the Core Processor, select the folder with the reconstructed 16-bit cross-sectional TIFF slices and the spreadsheet file. Select a couple of slices for inspection. Then select dark and white references as indicated in the spreadsheet file for wood density calculations.

In a new popup window, following the information from the spreadsheet file, select every core separately by drawing a circle or ellipse around it. Then click on Mass core extraction to extract all the cores in a given cylinder. In the Core Processor toolbox, click on Manual Tg correction.

Then select the extracted folder and ensure proper orientation of the transversal and radial plane of every core volume. To visualize grain direction from the bottom right plot, observe the presented slice and draw a line indicating grain direction. Double click to automatically rotate the core.

Then crop the core volume to get only wood and no other material. Open the Ring Indicator toolbox and select a multi-page TIFF file. Then, under a volume tab, inspect the graphical user interface in the transverse and radial plane.

For structural correction on the transverse and radial plane, click on the image to insert green bars starting with the pith and ending with the most recent ring. Once a green bar is placed on one plane, it automatically generates on other planes. Click Densitometry then Densitometry plot to calculate the density profile.

Create and plot a density profile by selecting Overlay plotting and then Plot density profile. Once the density profile is visualized, indicate all tree rings. Move the nodes at the end of the bar to change the angle.

Then change the bar position using the middle node and adjust the size of the nodes. Press Data, then Export. Press Rings followed by Export rings to ensure ring and fiber indications are written in the proper txt files.

Change the felling date to the year when the cores were taken from the living trees, or choose an appropriate date. In Overlay plotting, select Plot rings to display the years. Also, choose the plane to plot rings or the density profile.

After indicating two cores, open the Core Comparison toolbox for comparing the ring width series. Select the txt files to compare, then a screen displaying ring widths and cross-dating and statistical parameters such as Gleichlaufigkeit and Spearman correlation between individual series will open. Open a Ring Indicator instance to adjust the green bars and export them again.

Then maximize the Core Comparison screen and press the refresh button to reevaluate the metrics. Next, select Plotting and exporting, then Ring width to visualize the tree ring width, or TRW data. Click Plotting and exporting, then Export RW data to export TRW data in a spreadsheet or Tucson format.

Finally, select the other plotting, then export cluster data for obtaining mean density, MXD, MND, and quartile data per tree ring. This study demonstrates three levels of biomass estimation or tree growth increment at the inter-ring, ring, and anatomical scale. Radial and axial wood density trends in Terminalia superba demonstrated an increasing density trend from pith to bark and a higher wood density in the upper stem.

An example of chronology development with minimum density and maximum latewood density from Widdringtonia cedarbergensis is shown. A high resolution oak core scan demonstrated that earlywood and latewood vessels are segmented.