<meta charset="utf8"></head><body>Protocole pour la numérisation des cernes d’arbres du champ au laboratoire dans les études dendroécologiques

<ol>
	<li>Wimmer, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arthur+Freiherr+von+Seckendorff-Gudent+and+the+early+history+of+tree-ring+crossdating.">Arthur Freiherr von Seckendorff-Gudent and the early history of tree-ring crossdating.</a> Dendrochronologia. 19 (1), 153-158 (2001).</li><li>McGraw, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Andrew+Ellicott+Douglass+and+the+giant+sequoias+in+the+founding+of+dendrochronology.">Andrew Ellicott Douglass and the giant sequoias in the founding of dendrochronology.</a> Tree-Ring Res. 59 (1), 21-27 (2003).</li><li>Schweingruber, F. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Tree Rings and Environment: Dendroecology. , (1996).</li><li>Amoroso, M. 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S. F., Bj&#246;rklund, J., Schneider, L., Wegner, J. D., von Arx, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Towards+ROXAS+AI:+Deep+learning+for+faster+and+more+accurate+conifer+cell+analysis.">Towards ROXAS AI: Deep learning for faster and more accurate conifer cell analysis.</a> Dendrochronologia. 81, 126126 (2023).</li><li>G&#228;rtner, H., Lucchinetti, S., Schweingruber, F. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+new+sledge+microtome+to+combine+wood+anatomy+and+tree-ring+ecology.">A new sledge microtome to combine wood anatomy and tree-ring ecology.</a> IAWA J. 36 (4), 452-459 (2015).</li><li>G&#228;rtner, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+technical+perspective+in+modern+tree-ring+research+-+how+to+overcome+dendroecological+and+wood+anatomical+challenges.">A technical perspective in modern tree-ring research - how to overcome dendroecological and wood anatomical challenges.</a> J Vis Exp. 97 (e52337), (2015).</li><li>G&#228;rtner, H., Banzer, L., Schneider, L., Schweingruber, F. H., Bast, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparing+micro+sections+of+entire+(dry)+conifer+increment+cores+for+wood+anatomical+time-series+analyses.">Preparing micro sections of entire (dry) conifer increment cores for wood anatomical time-series analyses.</a> Dendrochronologia. 34, 19-23 (2015).</li><li>G&#228;rtner, H., Schneider, L., Lucchinetti, S., Cherubini, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advanced+workflow+for+taking+high-quality+increment+cores+-+new+techniques+and+devices.">Advanced workflow for taking high-quality increment cores - new techniques and devices.</a> J Vis Exp. (193), e64747 (2023).</li><li>Wang, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acoustic+measurements+on+trees+and+logs:+a+review+and+analysis.">Acoustic measurements on trees and logs: a review and analysis.</a> Wood Sci Technol. 47, 965-975 (2013).</li><li>Steenkamp, C. J., Van Rooyen, M. W., Van Rooyen, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+non-destructive+sampling+method+for+dendrochronology+in+hardwood+species.">A non-destructive sampling method for dendrochronology in hardwood species.</a> South Afr For J. 186, 5-7 (1999).</li><li>Toole, E. R., Gammage, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Damage+from+increment+borings+in+bottomland+hardwoods.">Damage from increment borings in bottomland hardwoods.</a> J For. 57, 909-911 (1959).</li><li>Grissino-Mayer, H. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+manual+and+tutorial+for+the+proper+use+of+an+increment+borer.">A manual and tutorial for the proper use of an increment borer.</a> Tree-Ring Res. 59 (2), 63-79 (2003).</li><li>Griffin, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gigapixel+macro+photography+of+tree+rings.">Gigapixel macro photography of tree rings.</a> Tree-Ring Res. 77, 86-94 (2021).</li><li>. LINTAB-Precision ring by ring Available from: <a target="_blank" href="https://rinntech.info/products/lintab/">https://rinntech.info/products/lintab/</a> (2003)</li><li>. Regent Instruments Available from: <a target="_blank" href="https://regentinstruments.com">https://regentinstruments.com</a> (2024)</li><li>De Micco, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intra-annual+density+fluctuations+in+tree+rings:+How,+when,+where,+and+why.">Intra-annual density fluctuations in tree rings: How, when, where, and why.</a> IAWA J. 37, 232-259 (2016).</li><li>Edwards, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intra-annual+climate+anomalies+in+northwestern+North+America+following+the+1783-1784+CE+Laki+eruption.">Intra-annual climate anomalies in northwestern North America following the 1783-1784 CE Laki eruption.</a> J Geophys Res Atmos. 126, e2020JD033544 (2020).</li><li>Levani&#269;, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ATRICS-A+new+system+for+image+acquisition+in+dendrochronology.">ATRICS-A new system for image acquisition in dendrochronology.</a> Tree-Ring Res. 63 (2), 117-122 (2007).</li><li>Garc&#237;a-Hidalgo, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CaptuRING:+A+do-it-yourself+tool+for+wood+sample+digitization.">CaptuRING: A do-it-yourself tool for wood sample digitization.</a> Methods Ecol Evol. 13 (6), 1185-1191 (2022).</li><li>Rodriguez, D. R. O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exploring+wood+anatomy,+density+and+chemistry+profiles+to+understand+the+tree-ring+formation+in+Amazonian+tree+species.">Exploring wood anatomy, density and chemistry profiles to understand the tree-ring formation in Amazonian tree species.</a> Dendrochronologia. 71, 125915 (2022).</li><li>G&#228;rtner, H., Farahat, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cambial+activity+of+Moringa+peregrina+(Forssk.)+Fiori+in+arid+environments.">Cambial activity of Moringa peregrina (Forssk.) Fiori in arid environments.</a> Front Plant Sci. 12, 760002 (2021).</li><li>G&#228;rtner, H., Lucchinetti, S., Schweingruber, F. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+perspectives+for+wood+anatomical+analysis+in+dendrosciences:+the+GSL1-microtome.">New perspectives for wood anatomical analysis in dendrosciences: the GSL1-microtome.</a> Dendrochronologia. 32, 47-51 (2014).</li><li>Maeglin, R. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Increment Cores: How to Collect, Handle, and Use Them (Vol. 25). , (1979).</li><li>Agee, J. K., Huff, M. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The Care and Feeding of Increment Borers. , (1986).</li><li> Phipps, R. L., , . <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Collecting, Preparing, Crossdating, and Measuring Tree Increment Cores (No. 85-4148). , (1985).</li><li>Cole, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Protection and Storing Increment Cores in Plastic Straws. 216, (1977).</li><li>Rossi, S., Anfodillo, T., Menardi, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trephor:+a+new+tool+for+sampling+microcores+from+tree+stems.">Trephor: a new tool for sampling microcores from tree stems.</a> IAWA J. 27 (1), 89-97 (2006).</li><li>Schneider, L., G&#228;rtner, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+advantage+of+using+a+starch+based+non-Newtonian+fluid+to+prepare+micro+sections.">The advantage of using a starch based non-Newtonian fluid to prepare micro sections.</a> Dendrochronologia. 31, 175-178 (2013).</li><li>G&#228;rtner, H., Nievergelt, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+core-microtome:+A+new+tool+for+surface+preparation+on+corse+and+time+series+analysis+of+varying+cell+parameters.">The core-microtome: A new tool for surface preparation on corse and time series analysis of varying cell parameters.</a> Dendrochronologia. 28 (2), 85-92 (2010).</li><li>McCarroll, D., Pettigrew, E., Luckman, A., Guibal, F., Edouard, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Blue+reflectance+provides+a+surrogate+for+latewood+density+of+high-latitude+pine+tree+rings.">Blue reflectance provides a surrogate for latewood density of high-latitude pine tree rings.</a> Arct Antarct Alp Res. 34 (4), 450-453 (2002).</li><li>Bj&#246;rklund, J., Seftigen, K., Kaczka, R. J., Rydval, M., Wilson, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+standard+definition+and+terminology+for+Blue+Intensity+from+conifers.">A standard definition and terminology for Blue Intensity from conifers.</a> Dendrochronologia. 85, 126200 (2024).</li><li>Van den Bulcke, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advanced+X-ray+CT+scanning+can+boost+tree+ring+research+for+earth+system+sciences.">Advanced X-ray CT scanning can boost tree ring research for earth system sciences.</a> Ann Bot. 124 (5), 837-847 (2019).</li></ol>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Core-microtome</td>
			<td>WSL</td>
			<td>https://www.wsl.ch/en/services-produkte/microtomes/</td>
			<td>Microtome to cut micro sections from increment cores</td>
		</tr>
		<tr>
			<td>Epson Expression 10000XL&#160;</td>
			<td>EPSON</td>
			<td>https://epson.com/Support/Scanners/Expression-Series/Epson-Expression-10000XL---Graphic-Arts/s/SPT_E10000XL-GA</td>
			<td>flatbed scanner</td>
		</tr>
		<tr>
			<td>GSC holder</td>
			<td>WSL</td>
			<td>in-house</td>
			<td>3D printed mount to fix cores for transport, preparation, analyses, and storage</td>
		</tr>
		<tr>
			<td>Skippy image capturing system</td>
			<td>WSL</td>
			<td>https://www.wsl.ch/en/services-produkte/skippy/)&#160;</td>
			<td>Image capturing system developed at WSL equiped with a 61 MP camera (Sony Alpha 7R IV and Sony FE 90mm f/2.8 Macro lens)</td>
		</tr>
	</tbody>
</table>

a new workflow for sampling and digitizing increment cores

The principle of dating tree rings by applying the cross-dating technique was introduced the first time by the Austrian forest scientist Arthur Freiherr von Seckendorff-Gudent in 18811. In the first half of the 20th century, this technique was reinvented by the &#34;Father of Dendrochronology&#34; Andrew Ellicott Douglass, who intensively applied it in dating archaeological sites and living trees2.
Nowadays, dendroecology, the research topic acting as a kind of environmental frame of dendrochronology, is defined as the study of tree rings and their inherent growth variations caused by ecological and environmental changes in time3. In dendroecological research, many other characteristics than ring-width variations, such as stable isotopes, late wood density, or cell characteristics within single rings, are used to correlate these data to environmental parameters to better understand the impact of environmental conditions on tree growth over time4. Through the ongoing integration of wood anatomical studies to dendroecological research, dendroecology research evolved in the last decade and is more than ever a backbone in reconstructing past climate conditions5,6,7,8.
Although the technical development regarding sample preparation and analysis, especially in wood anatomy, was strong in the last decade9,10,11,12,13,14, there was almost no real advance regarding the simplification of sampling techniques15. Despite, e.g., acoustic wave technology16, until nowadays there is no reliable &#34;non-destructive&#34; method to extract the characteristics of rings from trees.
Consequently, all tree-ring-related studies still rely on wooden samples taken from trees or shrubs taken at the sites of interest. When focusing on trees, the standard procedure is taking increment cores from stems15.
Taking cores by using increment corers is frequently expressed as a &#34;non-destructive&#34; technique17. Compared to taking disks from stems, this is correct; nevertheless, this sampling technique causes a hole in the stem of about 1 cm in diameter, mostly reaching beyond the pith of the stem3. The tree is able to close this wound on its own, but this process causes growth reactions, altering the common structure in the close vicinity of the wound as well as a more or less intense discoloration of the existing wood around the hole because of fungal diseases18,19. So, it should better be called &#34;minimally invasive&#34; rather than &#34;non-destructive&#34;.
The technique of taking increment cores evolved recently through the ability to use mechanical drills, resulting in higher quality samples, especially for wood anatomical analyses15. This procedure also saves a lot of time in the field compared to manual coring. What remained unchanged was the procedure of handling the cores, starting from the extraction from the tree to labeling, storing for transport, and preparing them in the lab for various possible analyzing techniques.
Cores still need to be packed in stable containers, such as straws made of plastics or paper, to prevent them from breakage during transport. Labeling the cores is done directly on the core using soft pencils or (more frequently) on the outside of each straw. When using plastic containers, the cores must be taken out after a short time to avoid the spread of fungi. So, the cores need to be taken out of the containers again. To stabilize the cores and to prevent them from bending when they start drying, the cores need to be fixed on a mount. This also helps with the subsequent surface preparation for further analyses. When doing so, the labels also need to be transferred to the respective mounts. A standard procedure is gluing the cores on wooden mounts or fixing them with tape in the rills of corrugated boards. Gluing them on wooden mounts is the most frequently used technique. Although this procedure is perfect for stabilizing and sanding or cutting the cores, it has several disadvantages regarding potential chemical, isotopic, and even wood anatomical analyses. Another disadvantage, despite the time required, is the error-prone transfer of the labels for each core to the new mounts.
In dendrochronology, ring-width measurements as a base for accurate dating are the backbone of all dendroecological studies20. Although many labs still rely on manual measurements using measurement tables, e.g., Lintab21 with attached binoculars, there is a trend of using flatbed scanners to digitize core surfaces and measure ring-width using software such as CooRecorder22 or WinDENDRO23. Unfortunately, these scanners, e.g., the widely used Epson Expression 10000XL do not have sufficient resolution to clearly depict structures as earlywood or latewood tracheids (Figure 1). For this reason, the resulting images are not suitable for recognizing difficult structures such as very narrow rings or density fluctuations, which are critical for an accurate cross-dating procedure without going back to the original cores using binoculars24,25.
Since high image resolution is an indispensable prerequisite for adequate image analyses in tree-ring science10, a new image-capturing system was developed at WSL (Skippy; https://www.wsl.ch/en/services-produkte/skippy/) to digitize tree rings on core surfaces using a digital camera resulting in images presenting a higher resolution than all existing flatbed scanners. This system was based on the idea of the ATRICS-system26, developed in 2007. Most recently, a simple but efficient image-capturing system comparable to the Skippy was presented as a self-assembly kit27.
Digitizing tree rings, i.e., reflected light image capturing, is an important step in creating high-resolution images of increment cores or disks to support a time-efficient, digitally based ring-width measurement. The system developed at WSL also allows taking images from long micro sections (up to 40 cm) using transmitted light. This additional feature is, for example, of interest for dendrogeomorphic applications to identify the onset of reaction wood in micro sections.
In the study, we present a protocol to ease the process of handling cores in the field and the lab. The base of the new technique presented is a reusable mount; the new GSC-holder G&#228;rtnerSchneiderCore (GSC) holder designed using 3D-modeling software and printed with a 3D printer. The GSC-holder allows for straightforward handling of the cores taken in the field without repacking or relabeling them. We also present an efficient new system for digitizing the prepared surfaces of the cores. This protocol spans the entire procedure from taking cores in the field to sample preparation, digitizing the core surfaces for subsequent analyses, and eventually storing them in an archive.

<meta charset="utf8"></head><body>Pleins feux sur l’auteur : Développement de dispositifs innovants pour faire progresser la recherche sur la dendroécologie et l’anatomie du bois

Un nouveau flux de travail pour l’échantillonnage et la numérisation des carottes d’incrément 

Here we present a new workflow from taking increment cores in the field, storing and transporting them to the lab, to digitizing their tree rings for ...

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Research

A New Workflow for Sampling and Digitizing Increment Cores

JoVE Journal

Environment

878 vues.  Swiss Federal Research Institute WSL. En développant de nouveaux appareils, nous avons l’intention de repousser les limites de la recherche sur les cernes des arbres. L’application de logiciels de modélisation 3D et d’imprimantes 3D permet un développement rapide et peu coûteux de nouveaux appareils. L’un d’entre eux est le système de capture d’images, Skippy, qui permet de numériser la surface du parcours d’incrément en haute résolution et en peu de temps.Habituellem...

Vidéo: Pleins feux sur l’auteur : Développement de dispositifs innovants pour faire progresser la recherche sur la dendroécologie et l’anatomie du bois

Here we present a new workflow from taking increment cores in the field, storing and transporting them to the lab, to digitizing their tree rings for further analyses for subsequent dendroecological analyses. The procedure involves the use of new sample carriers for increment cores. These new G&#228;rtner Schneider Core (GSC) holders are designed using three-dimensional (3D) modeling software and finally printed with a 3D printer. Using these mounts from the beginning in the field, the cores can directly be cut with a core microtome, and their surface can then be digitized without further rearrangement using a new high-resolution image-capturing system. They are thus available for direct analysis. This system allows digitizing tree rings from cores and disks, and also taking images from long micro sections (up to 40 cm) using transmitted light. This feature is of special interest for dendroecological and geomorphic applications to identify the onset of any disturbance in micro sections cut with a core-microtome.

We present a protocol to use 3D-printed mounts to fix increment cores in the field without the necessity of unpacking and gluing them on wooden mounts. The new GSC holder allows placing the cores in a core microtome to cut their surface and directly transfer them to digital image capturing.