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See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Received: 30 November 2021 | Accepted: 14 March 2022

DOI: 10.1111/2041-210X.13847

PR ACTICAL TOOLS

CaptuRING: A do-­it-­yourself tool for wood sample digitization

Miguel García-­Hidalgo1 | Ángel García-­Pedrero2,3 | Daniel Colón2 |

Gabriel Sangüesa-­Barreda1 | Ana I. García-­Cervigón4 | Juan López-­Molina1 |
Héctor Hernández-­Alonso1,5 | Vicente Rozas1 | José Miguel Olano1 |
Víctor Alonso-­Gómez6
1
EiFAB-­iuFOR, Universidad de Valladolid, Soria, Spain; 2Department of Computer Architecture and Technology, Universidad Politécnica de Madrid, Madrid,
Spain; 3Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain; 4Biodiversity and Conservation Area, Universidad Rey Juan
Carlos, Móstoles, Spain; 5Area of Ecology, Faculty of Biology, Universidad de Salamanca, Salamanca, Spain and 6Department of Applied Physics-­EiFAB,
Universidad de Valladolid, Soria, Spain

Correspondence
Miguel García-­Hidalgo Abstract
Email: [email protected]
1. Standard procedures to obtain high-­quality images of wood samples have be-
Funding information come a bottleneck in the digitization of dendrochronology. Digitization is cur-
Caja Rural de Soria, Grant/Award Number:
rently dominated by flatbed scanners, but the use of these devices is limited by
Cátedra de Conocimiento e Innovación
2021; Junta de Castilla y León, Grant/ sample length and surface flatness. Although several solutions based on digital
Award Number: IR2020-­1-­UVA08 and
photography have been published, they lack effective digitization processes or
OUTBREAK (VA171P20); Ministerio
de Ciencia e Innovación, Grant/Award are too expensive to be widely adopted.
Number: CGL2017-­87309-­P (MGH
2. Free open-­source software and hardware has emerged as an alternative to cre-
PRE2018-­0 84106) and PROWARM
(PID2020-­118444GA-­I 00); Universidad ate research tools that combine reduced costs with high reliability. Here we pre-
Politécnica de Madrid, Grant/Award
sent CaptuRING, an open-­source tool for wood sample digitization combining
Number: RP200060107
a do-­it-­yourself hardware based on Arduino® with a DSLR camera and a free
Handling Editor: Aaron M Ellison
open-­source software with an easy-­to-­use graphical user interface.
3. We compared CaptuRing with image acquisition from a standard flatbed scan-
ner Epson® V750PRO. CaptuRING outperforms scanner image resolution and
sharpness, while it removes sample size limitations. Moreover, CaptuRing per-
forms this task in less than half of the time needed by Epson® V750PRO flatbed
scanner.
4. CaptuRING emerges as a reliable and low-­cost tool to capture high-­resolution
images of wood samples boosting current digitization processes. The combina-
tion of free open software and hardware empowers dendrochronology to ad-
vance in wood sample digitization.

KEYWORDS
dendrochronology, DIY, hardware, open source, sample digitization, software, wood cores,
wood slices

This is an open access article under the terms of the Creative Commons Attribution-­NonCommercial-­NoDerivs License, which permits use and distribution in
any medium, provided the original work is properly cited, the use is non-­commercial and no modifications or adaptations are made.
© 2022 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Methods Ecol Evol. 2022;13:1185–1191.  wileyonlinelibrary.com/journal/mee3 | 1185

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1186 Methods in Ecology and Evolu on García-­Hidalgo et al.

1 | I NTRO D U C TI O N Digital photography has appeared as an alternative to scanning.

Some previous studies have used digital single-­lens reflex (DSLR)
Biodiversity studies have recently evolved thanks to technological ad- cameras to capture tree core images (Fonti & García-­González, 2008;
vances in digital real-­time data sources. Data capturing from satellites Souto-­Herrero et al., 2018). However, the first published approach
(http://www.coper​nicus.eu/) to microscopic technology (Weber & for core digitization was ATRICS (Levanič, 2007) in which Levanič
Huisken, 2011) can be affordable and provide immediate digital informa- proposed a video camera assembled to a stereoscope which digi-
tion at multiple scales. However, due to the recent appearance of these tized tree core as it was moved by a worm gear. Recently, Griffin
data sources, they do not provide long temporal records, and other et al., 2021 published Gigapixel, which reaches an impressive image
sources of information to complete this shortfall (Olano et al., 2021) are quality with very high resolution (19,812 dpi, 1.28 μm per pixel) in
therefore required. This is the case with dendrochronology, the science the verge of being able to analyse xylem cellular structure. Despite
that deals with tree rings, which provides a long-­term perspective in Gigapixel being based on free open software, final image hosting
ecological and biodiversity research through analysis of plants with an- requires the payment for cloud computing services, and hardware
nual secondary growth increments (Schweingruber, 2012). costs ($70,000) are beyond the budget of most research groups, es-
Dendrochronology is following the scientific world's relentless pecially in developing countries.
step towards digitization (Schmidt et al., 2016). However, techniques Free open-­source software and hardware have emerged as in-
for cross dating tree-­ring series and ring width measuring still remain novative systems to make research with precise and accurate open
in the analogical world. Measuring processes from wood samples, tools more accessible (Gibney, 2016). Accordingly, open-­source
generally increment cores, are mainly performed using a stereo- packages for different dendrochronology tasks have been published
scope and different, generally expensive, tree-­ring measuring stages (Campelo et al., 2012; García-­Hidalgo et al., 2021; Rademacher
(e.g. Lintab: https://rinnt​ech.info/, Velmex™: https://www.velmex. et al., 2021). However, there is currently a lack both in proprietary
com/). These devices convert lead screw shifting into ring width and open specific software focused on image acquisition process.
measurements which are digitally saved. Alternatively, dendrochro- The aim of this manuscript is to present an open-­source tool that
nologists have a wide array of reliable software to extract ring width generates high-­quality images in a fast and low-­cost way to boost
measurements from digitized images of wood, transforming pixels the digitization of wood samples. In order to fit with this aim, we
into micrometres (e.g. MTreeRing: Shi et al., 2019, Coorecorder™: combine an affordable do-­it-­yourself hardware with open-­source
Larsson, 2014, Windendro™: Instruments, 2007). However, the full software graphical user interface (GUI) as an effective digitization
popularization of the use of these tools is hampered by our limited tool for tree-­ring studies. Hardware can be assembled with just basic
capacity to digitize images of wood with enough quality to serve as skills, whereas CaptuRING software provides an effective and intu-
a digital model in a fast and low-­cost procedure. Moving to ‘digital itive digitization of the core samples. In the following sections, we
cores’ is not only an issue of novelty, as it would open the avenue explain the main components, software options and availability of
to get a ‘digital twin’ that could dynamically replicate responses to CaptuRING System.
intrinsic and environmental variables from a physical sample into the
digital world (Fuller et al., 2020). Digital models enable storage of
samples in an accessible digital format in private or public resource 2 | C a pt u R I N G S YS TE M
banks, from which samples can be easily available for checking and
reusing for new analysis. Furthermore, effective digitization of sam- CaptuRING basic functionality guides the sample across the visual
ples promotes the exchange of information between researchers range of the DSLR camera, as well as controlling the image acquisi-
(Contreras, 2018; Davies et al., 2017). tion and storage. The CaptuRING tool is comprised of a DIY hard-
The main physical obstacles to core digitization are their ex- ware module and a software module. Since a computer must be in
tremely large structure and their having a surface that is often use for the capturing process, the system is run using a Raspberry
not completely flat. Flatbed scans have dominated the acquisition Pi (https://www.raspb​errypi.com/) to optimize the digitization pipe-
of digitized wood samples, especially with the availability of high-­ line, although CaptuRING software is a cross-­platform tool and can
resolution scanners (up to 6,400 dpi, 3.9 μm per pixel). However, be run in any operative system.
core scanning at such high resolutions is very time-­consuming and
those extremely high aspect ratio images can cause problems due
to the high computational requirements for image exportation. 2.1 | Hardware
Moreover, since scanners require totally flat samples, a requirement
that is rarely fulfilled in sanded wood samples, the output image can Hardware components of CaptuRING arrange the sample by mov-
contain portions that are out of focus. Additionally, the size of scan- ing it at equal steps through the camera's visual field during image
ner determines the maximum length of the image capturing limiting capturing (Figure 1). The sample holder (Supplementary Material
their use for large cores or slices. [Correction added on 8 April 2022, 1) is carried by a ball screw Linear Motion Guide (50 cm/stepper
after first online publication: the unit 3.9 m per pixel has been cor- motor mod. 42BYGH48; 1.8, 1.2 A, 0.4 Nm, DFA), hereafter spin-
rected to 3.9 µm.] dle, which is moved by the stepper motor. That motion is controlled
 |

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García-­Hidalgo et al. Methods in Ecology and Evolu on 1187

F I G U R E 1 CaptuRING device and components' connection scheme

TA B L E 1 CaptuRING components and estimated price them to be used for image acquisition in dendrochronology or any se-
Component Price (€) quential image capturing purposes. CaptuRING motion hardware can
be acquired for <300 €, meanwhile the complete digitization device
CaptuRING motion hardware 284–­407
from scratch can be purchased for approximately 1,700 €. All the com-
Photography enlarger base 50–­60
ponent specifications and the estimated prices are listed in Table 1.
Led lighting 80–­100
C-­Beam linear actuator (500 mm) + NEMA 23 100–­150
stepper motor
2.2 | Software
Endstop switch 1–­2
Linear rails (2) 20–­4 0
CaptuRING software controls image capturing by a DSLR camera
Driver IC for stepper motor 3–­5
while the sample goes through its visual field. This software is writ-
Arduino® based 3D printer controller 20–­3 0 ten in Python (http://www.python.org) and controls spindle move-
Power supply (12 V DC/150 W source) 10–­20 ment with Arduino® and DSLR camera shooting with gphoto2 library
Sample holdera DIY (https://pypi.org/proje​c t/gphot​o2/). The whole capturing process
Rail adaptera DIY is controlled by a specific interface made with the use of PyQt5 li-
Optical and controlling devices 1,450–­1,850 brary (https://pypi.org/proje​c t/PyQt5/). CaptuRING code is avail-
Raspberry Pi Kit (with microSD, power source, 100–­150 able through Zenodo (10.5281/zenodo.6351358) (García-­Hidalgo,
cables and case)b García-­Pedrero, Colón, Sangüesa-­Barreda, Rozas, et al., 2022).
Peripherals (screen monitor, keyboard and 150–­200 The interface consists of just one window in which the user
mouse)b enters hardware and sample characteristics (Figure 2). The user
DSLR camerab 800–­1,000 completes the ‘Options’ box with CaptuRING hardware settings ac-
b
Camera lens 400–­500 cording to the device characteristics. Although these Options can be
a
Do-­it-­yourself with a 3D printer according Supplementary Material 1
changed anytime, they are saved for future CaptuRING use. In the
design. ‘Image Shooting’ box, the user enters sample name and size. Sample
b
Component election may diverge from user objectives and name must be confirmed by clicking the ‘Name It!’ button before
requirements. image capturing. Thus, a specific folder with sample name is created
and the digitized images will be saved there. Once the sample digiti-
by an Arduino® 3D printer controller (MKS-­GEN L V1.0) (https:// zation is completed, the user can change the sample name and size
www.ardui​no.cc/) which obtains the information from the end of for the next process.
track sensor and the computing system, a Raspberry Pi 4 model B.
All those driving components are, in addition to the camera, set up in
association with a photographic enlarger base (Figure 1). 2.3 | Acquisition process
The Raspberry Pi comprises every control by sending orders
via USB to the 3D printer controller and to the DSLR camera (Nikon The wood increment core must be mounted and sanded with pro-
D7500 with Tokina 100 mm f/2.8 ATX M Pro D Macro lens) using the gressive grain sizes as in standard dendrochronological procedures.
CaptuRING software. Although those hardware elements are not made For an optimum acquisition, we highly recommend reducing illumi-
specifically for scientific tasks, the software component can manage nation to increase contrast and obtain sharper images. Once the
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1188 Methods in Ecology and Evolu on García-­Hidalgo et al.

sample is placed on the device at the sample holder, the user enters 3 | CO M PA R I S O N W ITH FL ATB E D
sample name and length in millimetres in the interface. Additionally, SCANNER
process parameters for mismatched position (offset), screw speed,
step size, spindle size or platform size can be modified by the user Increment cores from conifer and broadleaved species were se-
depending on hardware characteristics. Once the sample size is lected to test image acquisition differences using a flatbed scanner
entered and name is confirmed by clicking the ‘Name it!’ button, Epson® Perfection v750 PRO (maximum resolution 6,000 dpi) and
‘CAPTURE’ runs image acquisition. CaptuRING. This flatbed scanner is a common digitization tool in
CaptuRING takes a series of sequential and partially overlapped dendrochronological research (Marcelo-­Peña et al., 2019; Navarro-­
photographs after individually autofocussing for each image. The Cerrillo et al., 2020; Venegas-­González et al., 2015).
autofocus process is particularly important when the sample is The samples were mounted and sanded at progressive grain sizes
not totally flat and the distance from the camera lens may vary at (from 80 to 800) before digitization. Eight incremental cores were in-
different points of the sample surface. Subsequently, the camera dividually digitized with each device and information recorded about
takes one picture when the core stops in its stepped-­carried way sample characteristics (species, length), image resolution (in dots
across the platform. During the capturing process, the individual im- per inch) and time (in seconds) for image acquisition (Supplementary
ages are saved in a sample-­specific-­named folder with an individual Material 2). Since the scanning process is computationally limited to
and consecutive name. When the capturing process is finished, the 20,000 pixels width and 30,000 pixels length by Epson Scan software®,
tool comes to the starting position to restart with the next sample. complete sample cores were scanned at feasible maximum resolution.
CaptuRING captures and saves sequential images, but the whole CaptuRING shooting and image stitching by using PTGui v8.3 (New
sample image must be generated by using a stitching software. House Internet Services BV, Rotterdam, NL) was measured in order to
There are a wide range of tools to complete this step in FOSS (e.g. get comparable results using both CaptuRING and scanning digitization
ImageJ: Schindelin et al., 2012 or OpenCV: https://opencv.org/) as methods for the complete sample. Complete images are available at
well as proprietary software already reviewed for quantitative anat- Zenodo (10.5281/zenodo.6365664) (García-­Hidalgo, García-­Pedrero,
omy (von Arx et al., 2016). Due to the limited hardware capabilities in Colón, Sangüesa-­Barreda, García-­Cervigón, et al., 2022).
Raspberry Pi, image files should be shared with a standard computer CaptuRING increases resolution acquisition from 4200 dpi max-
to optimize the whole capturing process. imum resolution at scanning with Epson Perfection V750PRO up to
5339 dpi (4.76 μm per pixel) with a 24MP non-­professional DSLR
camera (Nikon D7500). [Correction added on 8 April 2022, after
first online publication: the unit 4.76 m per pixel has been corrected
to 4.76 µm.] Thus, this tool provides sharper images in contrast to
the classical blurry scanned images (Figure 3). At the same time, av-
erage image acquisition time decreases by 60% using CaptuRING
(Figure 4). Furthermore, CaptuRING removes the sample size barrier
associated with flatbed scanning, usually 216 × 297 mm at maximum,
by using a lead screw of the desired length.
The final resolution and quality of the CaptuRING image depend
on camera and lens features. Sensor size modifies lens magnification
power, APS-­C cameras have a magnification factor (1.5–­1.6) when
compared to full frame cameras, albeit at the expense of image
quality (Santosi et al., 2017). Additionally, the dynamic digital cam-
era industry improves image quality and resolution at an impressive
speed. Finally, lens election is critical and moving from the 1:1 macro
standard to super macro lenses dramatically increases magnifica-
tions up to 5:1 albeit at the cost of notably reducing depth of field.

4 | LI M ITATI O N S A N D I M PROV E M E NT
P OTE NTI A L

CaptuRING has been already tested by obtaining high-­resolution im-

ages from more than 3800 tree cores. During its use, some issues and

F I G U R E 2 CaptuRING interface. Options section must be pitfalls were tackled in order to produce a robust and reproducible
completed with hardware requirements while Image Shooting protocol for obtaining accurate digitized samples. The main obsta-
section controls sample digitization cles encountered were related to sample flatness, image stitching and
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García-­Hidalgo et al. Methods in Ecology and Evolu on 1189

F I G U R E 3 Detailed images from wood

samples obtained with CaptuRING (left)
and Epson® Perfection V750PRO (right)
of Fagus sylvatica L. on the top and Pinus
nigra Arn. at the bottom

F I G U R E 4 Processing times for

digitization of tree cores with different
380
length by using Epson® Perfection
V750PRO (green triangles) and
340
CaptuRING at 5,931 dpi (red dots). Linear
regression models are shown with 95%
300
confidence interval (grey) for maximum
Digitization time (s)

resolution data. Non-­filled triangles

260
represent scanning times at 2,400 dpi due
to scanning size limitations for 3,200 dpi
220

180

140

100

60
120 160 200 240
Sample length (mm)

scale. As a result of this assessment, we noticed that proper sample detailed metadata file could enable the standardization across
preparation is essential in order to minimize future artefacts in the labs. Developing specific software for automatic stitching process
generated images. Furthermore, sample flatness minimizes the need attached to CaptuRING could be also relevant. Moreover, the de-
of autofocus, which could reduce image stitching quality. We use a sign of a specific sample holder for wood slices of different sizes will
thickness planer process prior to sanding. In this way, we minimize vastly increase the possibilities of this tool. Resolving these issues
the need of autofocus. Another point of potential difficulty is related with open-­source tools will optimize the entire digitization process
to the stitching process, where image artefacts can appear. In order and could increase the possibilities of CaptuRING becoming widely
to avoid them, in case of using PTGui, we highly recommend the use used for any wood digital sampling.
of the standard protocol developed by von Arx et al. (2016). In any
case, maximizing the number of control points in the overlapping im-
ages minimizes the risk of image artefacts. Finally, scale is another 5 | CO N C LU S I O N S
important issue, as even when images are nearly at the same scale,
small differences in focal distance can lead to measurement errors. CaptuRING does not have the same susceptibility to hardware
So, we attach a graphical scale on the CaptuRING sample holder that limitations or flawed flatness as flatbed scans do and streamlines
allows to measure the effective resolution of each sample. the process of automatically storing each digital sample and associ-
There is an ample room for further improvement. Light control ated metadata in optimized time, being more than 50% faster than
is a critical field. We are currently developing a system to isolate a flatbed scanner in our comparative tests. Moreover, CaptuRING
the sample and the camera lens tandem from environmental light, increases resolution acquisition from 4200 dpi maximum resolution
which will allow the user to standardize lighting by removing dif- with scanning to 5931 dpi with a 24 MP non-­professional DSLR
fuse light. File management is also important, and developing a camera, controlling sample illumination and without any sample
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1190 Methods in Ecology and Evolu on García-­Hidalgo et al.

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