A New Workflow for Sampling and Digitizing Increment Cores

By developing new devices, we intend to push boundaries in tree ring research. The application of 3D modeling software and 3D printers allows a fast and cheap development of new devices. One of those is the image capturing system, Skippy, which allows digitizing the surface of increment course in high resolution and short time.

Usually when sampling in dendroecology, dendrogeomorphology, or dendroclimatology, we sample trees in remote regions like very high latitude regions, and where also climatic conditions are harsh. So saving time is very important. And adopting this protocol, we will save time, which is money.

Applying our protocol will allow to produce bigger data sets in shorter time. To begin, open the 3D model of the holder in a Slicer program compatible with a 3D printer. Create a print file that can be read by the 3D printer, ensuring it is saved as a G-code file.

Using a memory card or a USB stick, activate the print file on the 3D printer. Once the holder is printed, wait until it cools to room temperature. Remove the plate the holder sticks to from the printer, bend the plate slightly until the holder separates from the surface.

Lastly, remove all excess threads or attachments from the holder. To begin, take a cordless drill with a torque booster and an increment core. After selecting the coring position, place the core perpendicular to the growing axis of the stem.

Then start coring until the core reaches at least half of the stem diameter. Check the depth by holding the extractor alongside the core. If using a cordless drill, remove the drill.

Place the handle on the core. Take the extractor with the open side facing upwards and insert it fully into the core. Then turn the increment core backward one full turn to break the core off the stem.

After that, take out the extractor, including the core. Now, remove the core from the extractor. Check the fiber direction of the core to ensure an upright orientation when placing the core in the holder.

Afterward, place the core on top of the holder with the fiber direction upright. Press on top of the core with all fingers until it slides into the holder. Using a soft pencil, label the core on the side of the holder.

Place the holder with the core into the transport box, and close the cover of the transport box. To begin, place a steel box with a lid fitted with a valve for a vacuum pump connection on a hot plate. Fill the box up to approximately two centimeters with paraffin and wait until it has completely melted.

Take the mounted cores out of the transport box. Place the holders with the cores in the liquid paraffin and close the lid. Then start the vacuum pump and apply a constant light vacuum to the container.

After stopping the vacuum pump, open the lid. Take out the holders with the cores, place them on a grid and let them cool down. If needed, remove surplus paraffin from the sides of the holder.

Remove the mounted cores from the transport box or the paraffin bath. Place the holder with the core in the sample holder of a core microtome. Ensure the late wood of the rings faces toward the blade.

Now, tighten the screws of the sample holder until the core holder is completely secure. Lift the sample holder until the core slightly touches the blade. Pull the blade over the entire extent of the core to cut off the first part of the top.

Then push back the knife behind the core, and lift the sample holder a few microns. Once the surface is cut as intended, remove the core holder from the sample holder of the microtome. To begin, place the core holder with the plain core surface on the table of an image capturing system such as the WSL Skippy system.

Align the core holder with the moving direction of the table or camera. Position the table with the core holder below the camera, so the outermost ring is in the center of view under the camera objective. Now place a scale next to the onset of the core and take an image for calibration purposes.

Define the length of the core in the software, and start the image capturing process. Once the last image is taken, the table moves back to the starting position. Then remove the sample from the table.

Place the next holder below the camera. Next, use distortion free stitching software such as PD GUI to combine the single images into one final image of the core surface. Take the analyzed cores in the holder and place them in the portable storage rack printed with a 3D printer.

Label the rack to identify the cores from the outside. Store the rack on a shelf, or any other available archive. The high resolution camera system achieved a real resolution of 6, 500 DPI compared to 1, 825 DPI from a flatbed scanner.

The camera system provided clear images of single cells enabling precise identification of ring boundaries. The system facilitated imaging of micro sections of tree cores up to 40 centimeters with transmitted light, which is useful for dendrogeomorphology studies.