Convolutional Neural Networks for Knot Measurement in Tomographic Images of Wood Logs

This work provides novel approaches to knot diameter and DKB coordinate regression in wood logs by exploiting Convolutional Neural Networks (CNNs). One of the proposed procedures, concerning the subsequent application of a CNN for status classification to CT voxel sub-blocks containing consecutive portions of each knot, yields promising results and is computationally fast enough to be employed in in-line applications, both in terms of diameter regression and status estimation

Open tools for dendrochronology. Advances in sample digitization and deep learning methods for image segmentation

Dendrochronological techniques are paramount in forest research. The current climate change scenario and the central role of forests in biogeophysical cycles enforce the importance of novel techniques to get accurate data from trees and their relationship with the environment in faster ways. Recent technological advances and the place of open source software and hardware are making free, user-developed tools for forest research available to the research community. The aim of this Ph.D. thesis is the development of tools for image acquisition and data collection in dendrochronology based on open source software and hardware. Thus, four different tools for dendrochronological research are presented in five different chapters. The first chapter focuses on the development of a do-it-yourself tool based on open source hardware for image acquisition and wood sample digitization at high resolution. We used open hardware equipment from Arduino and Python programming to develop CaptuRING and published the entire free open source tool as: "CaptuRING: A Do-It-Yourself tool for wood sample digitization" in Methods in Ecology and Evolution, 2022; 13:1185-1191. Furthermore, the original software was registered in the Registro General de Propiedad Intelectual (00/2022/737) of Ministerio de Cultura y Deporte (Spain). The second chapter presents "How to build and install your own CaptuRING". This contribution presents a series of videos with a step-by-step guide to promote the use of CaptuRING in the research community. The manuscript and related videos have been submitted for publication. The third chapter describes ρ-MtreeRing. This free and open-source software, which is written in R, analyzes X-ray films from dendrochronological samples to get microdensity values automatically segmented through a graphical user interface. The open source tool and manuscript are published as: "ρ-MtreeRing. A graphical user interface for X-ray microdensity analysis" in Forests. 2021; 12(10):1405. The fourth chapter describes the potential of deep learning methods to automatically segment xylem vessels. We trained three different convolutional neural networks to segment vessels in stained wood microsections using the Keras framework in Python. Our results demonstrate the potential of these techniques to automatically segment xylem vessels and overcome derived problems from image illumination, which hamper segmentation using classical image segmentation methods. The manuscript is published as "Convolutional neural networks for segmenting xylem vessels in stained cross-sectional images" in: Neural Computing & Applications, 2020; 32:17927-17939. The fifth chapter develops an algorithm to delineate annual ring limits in stained wood microsections of a species with diffuse porous wood using convolutional neural networks. We used Python for image processing and the Keras framework for the algorithm training. The results show the ability of this techniques to obtain accurate tree ring segmentation for quantitative wood anatomy, reaching similar or even outperforming conventional manual delimitation in most of the evaluated cases. The results of this chapter will be presented in the manuscript "Deep Learning for ring bordering in stained cross-sectional images". This PhD Thesis presents four open source tools to get accurate information from wood features to unveil how trees respond to the environment. From digitization at macroscopic perspective, automatic data collection and the development of feature segmentation on microscopic samples. The presented four novel dendrochronological tools based on open source software facilitates forest research in the current climate change scenario.Las técnicas dendrocronológicas son fundamentales en la investigación forestal. El escenario actual de cambio climático y el papel central de los bosques en los ciclos biogeofísicos subrayan la necesidad de nuevas técnicas para obtener de un modo ágil datos precisos de los árboles y de su relación con el medio ambiente. Los recientes avances tecnológicos, además de la disponibilidad actual del software y el hardware de código abierto están poniendo a disposición de la comunidad investigadora herramientas gratuitas desarrolladas por los usuarios para la investigación forestal. El objetivo de esta tesis doctoral es el desarrollo de herramientas para la adquisición de imágenes y la recogida de datos basadas en software y hardware de código abierto para el estudio dendrocronológico. Esta tesis presenta cuatro herramientas diferentes para esta rama científica en cinco capítulos diferentes. El primer capítulo se centra en el desarrollo de una herramienta "hágalo usted mismo" basada en hardware de código abierto para la adquisición de imágenes y la digitalización de muestras de madera a alta resolución. Usamos equipos de hardware abierto de Arduino y programación de Python para desarrollar CaptuRING y publicamos la herramienta completa de código abierto como: "CaptuRING: A Do-It-Yourself tool for wood sample digitization" en Methods in Ecology and Evolution, 2022; 13:1185-1191. Además, el software original fue registrado en el Registro General de Propiedad Intelectual (00/2022/737) del Ministerio de Cultura y Deporte (España). El segundo capítulo presenta "Cómo construir e instalar su propio CaptuRING" ("How to build and install your own CaptuRING"). Esta contribución presenta una serie de vídeos con una guía paso a paso para promover el uso de CaptuRING en la comunidad investigadora. El manuscrito y los vídeos relacionados se han enviado para su publicación. El tercer capítulo describe ρ-MtreeRing. Este software gratuito y de código abierto, que está escrito en R, analiza imágenes de rayos X de muestras dendrocronológicas para obtener valores de microdensidad automáticamente segmentados a través de una sencilla interfaz gráfica de usuario. La herramienta de código abierto y el manuscrito se publicaron como: "ρ-MtreeRing. A graphical user interface for X-ray microdensity analysis" en Forests. 2021; 12(10):1405. El cuarto capítulo describe el potencial de los métodos de aprendizaje profundo para segmentar automáticamente los vasos del xilema. Entrenamos tres redes neuronales convolucionales diferentes para segmentar vasos en cortes histológicos de madera utilizando el marco Keras en Python. Nuestros resultados demuestran el potencial de estas técnicas para segmentar automáticamente los vasos del xilema y superar los problemas derivados de la iluminación de la imagen, que dificultan la labor de métodos clásicos de segmentación de imágenes. El manuscrito se publicó como "Convolutional neural networks for segmenting xylem vessels in stained cross-sectional images" en: Neural Computing & Applications. 2020; 32:17927-17939. El quinto capítulo desarrolla un algoritmo para delinear los límites anuales de los anillos en cortes histológicos de una especie con madera difuso-porosa utilizando redes neuronales convolucionales. Se utilizó Python para el procesamiento de imágenes y el marco Keras para el entrenamiento del algoritmo. Los resultados muestran la capacidad de estas técnicas para obtener una segmentación precisa de los anillos de los árboles para la anatomía cuantitativa de la madera alcanzando, en la mayoría de los casos evaluados, un rendimiento similar o incluso superior a la delimitación manual convencional. Los resultados de este capítulo se presentarán en el manuscrito "Deep Learning for ring bordering in stained cross-sectional images". Esta Tesis Doctoral presenta cuatro herramientas de código abierto para obtener información precisa de las características de la madera investigar cómo los árboles responden al entorno facilitando la investigación en el actual escenario de cambio climático.Escuela de DoctoradoDoctorado en Conservación y Uso Sostenible de Sistemas Forestale

Neutron imaging versus standard X-ray densitometry as method to measure tree-ring wood density

Neutron imaging is a new non-destructive testing method in wood science. It is similar to X-ray methods but with differing sensitivities for different elements. In this study, neutron imaging was used to ascertain the density profiles of thin spruce samples and compared with results generated with standard X-ray microdensitometry. Data obtained through neutron imaging were similar to those resulting from the X-ray method. The advantage of neutron imaging is its higher sensitivity to some elements such as hydrogen. Together with the high neutron-sensitivity of the applied detectors (imaging plates) this makes shorter exposure times possible, and yields more detailed information on the inner composition of wood. X-ray film, which is still most commonly used in X-ray densitometry, has the disadvantage that the relationship between the optical density of the film and the density of wood is non-linear. This means that corrections and calibration with step wedges are necessary, whereas with neutron imaging the digital values can be used directly to calculate the density at a certain point of the specimen. Thus neutron imaging appears to be an appropriate method, which can be used as complement to established X-ray methods for fast and straightforward investigations of tree rings, growth zones and wood densit

Análisis de metodologías para la evaluación de la madera juvenil en la calidad de la madera

On conifer species, when growing, on the inner part of the log closer to the pith they produce wood with different characteristics, which show rapid and progressive changes in the rings outward from the pith in a transverse direction until a point is reached where the properties are stabilized. The area closer to the pith is called juvenile wood (JW) to distinguish it from the mature wood (MW). The JW is characterized by having a celular structure with smaller tracheid length, lumen diameter, wall thickness, transverse shrinkage, stiffness and cellulose/lignin ratio. Other properties are lower, such as density and mechanical properties but others, such as spiral grain and microfibril angle (MFA) are higher. One phenomenon sometimes related to JW is the presence of wider growthrings and high levels of compression wood, although these last two relationships are not mutually exclusive. The transition year (TY) between JW and MW can be found by analyzing all these different properties. The boundary tends to change according to the wood property studied with variable patterns from pith to bark. All of these characteristics have undesirable effects on the physical-mechanical and technological properties of the material for solid dimension lumber. Also, the higher the proportion of JW, the greater incidence of different drying distortions such as spring, bow, crook and twist resulting in diminished prospects for profitable end use and economic return for solid wood products. Different explanations to the presence of these variations have been proposed and different names have been given to these two areas that can be differentiated in transversal direction of the tree at any height. When considering the longitudinal variation, the nomenclature usually employed is corewood (CW) and outerwood (OW). But in this Thesis, we will use the JW/MW nomenclature as the Spanish industrial sector still uses it. There are several studies assessing the importance of juvenile wood for solid dimension lumber in Spain. But not much studies have been carried out on Mediterranean conifers regarding the effect of the silviculture on the amount of JW present on the bole. Basic specific gravity, MFA and densitometry have been extensively used as indicators of JW presence. In this Thesis different methodologies are studied for JW determination on Pinus nigra and Pinus sylvestris with different silvicultural management and those results are compared with the ones obtained from densitometry. The influence of silviculture on the TY in black pine and Scots pine stands in Spain using densitometry, is studied. This analysis is done using a segmented linear mixed model including the analysis of the different covariate effects, included in the models, on density. Also, the variations on the JW volume and tree taper produced depending on the silvicultural practices using latewood (LW) density radial variation, is considered. Other objective was to see if at basal height it is possible to estimate a TY, by means of the accumulated yearly height growth that can be related to the one obtained for yearly LW and medium density on Scots pine and black pine. It is assessed the feasibility of using multipoint near infrared spectra (NIRs) to differentiate between JW and MW. On the same way, the potential of the near infrared hyperspectral imaging (NIR-HI) for semi-automatic identification of JW and MW moieties carried out in Scots pine is also assessed. Finally, it is done a study of radial and angular shrinkage patterns in the transversal direction along different heights of the bole. Based on the results on shrinkages, the JW/MW areas obtained, are related to the ones obtained through densitometry. When assessing the JW area on a log, micro X-ray densitometry is a suitable method for its study, results showed that the best density trait for automatization of the process is LW density. If assessing the TY by increment cores, which can be done on standing trees, the pith needs to be in the extracted core in order to assess the boundary correctly. The function developed for segmented mixed models, provides a powerful and more stable tool to predict the TY in a large number of samples using LW density profiles. Drought index is relevant for the modelling affecting LW density, on the slope on the MW or the density in TY determination. Up to a height of 9 meters TY was reached prior to the implementation of any silvicultural treatment, so further sampling is necessary to assess whether any treatment could influence or shift the transition year outside the part influenced by the crown. However, within the crown and in the case of PN, pruning was found to affect the TY because the LW density required to reach it increased, thus delaying the TY and increasing LW density. In both pine species, thinning seems to have a significant albeit slight negative effect on LW density, while the thinning and pruning combined seemed to have a small positive effect on it, compared to the control group. These results presented here may vary depending on the intensity and the timing of thinning, as well as on the amount of green pruning carried out. The growth response after silvicultural treatments show that the amount of JW is reduced in percentage as total volume increases with any silvicultural treatment applied, for both species, in Mediterranean forests. The TY calculated using Chapman-Richards growth functions on the accumulated height increments, does not fit the estimation of the TY obtained through density for the Spanish provenances studied of Scots and black pines. The calibration between measurements obtained with multipoint NIRs and density data derived from micro X-ray densitometry has been found difficult to obtain good enough results. On the other side NIR-HI can be calibrated with μXRD results and the JW, MW and transition point (TP) between both, can be determined on the transversal section of the tree. The results are independent from the silvicultural treatment applied in the Scots pine plantations studied. The principal component analysis was a useful and easy way to provide additional information on the presence and location of compression wood. The partial least squares discriminant analysis approach was the best procedure for detecting the TP between JW and MW, when the EW and LW were evaluated separately. Every strip was classified within ±1 annual ring difference compared with the LW. The biggest margin was ±2 annual rings. A previous automatic classification, by combination with a partitional k-means unsupervised classification, between EW and LW, would probably improve the results and could lead to a better automation of the process. Radial shrinkage tends to be in the first rings, up to the first 8 rings near the pith, between 4 and 9 %, decreasing until it stabilizes around 3%. Regarding the angular shrinkage, is close to 0% or even negative near the pith and increases until a certain ring (9-11) when it becomes more or less stable at around 2 %. These results are valid all along the bole, being greater and the transition produced earlier in radial shrinkage than in the angular one in each height studied. No general patterns can be seen along the same tree at the different heights sampled. Applying silvicultural treatments seems not to have any significance on the radial and angular shrinkage variation. If density is not an issue for the strength grading of solid dimension timber, the volume regarding the area where the shrinkage is stable suggest that, if the longitudinal shrinkage follows a similar pattern, the area that could be segregated for higher quality is bigger than the one provided by latewood density radial variation.En las distintas especies de coníferas, en la parte interna del tronco más cercana a la médula se genera, al crecer, madera que presenta cambios rápidos y progresivos en los sucesivos anillos hacia la corteza en dirección transversal, hasta que se alcanza un punto donde las propiedades se estabilizan para el resto de los anillos. El área más cercana a la medula se llama madera juvenil (JW) para distinguirla de la madera madura (MW). La JW se caracteriza por tener una estructura celular con menor longitud de traqueidas, diámetros de lúmenes, espesor de pared, contracción transversal, rigidez y relación celulosa/lignina. Unas propiedades que también son más bajas serían la densidad y las propiedades mecánicas, pero otras, como el grano en espiral y el ángulo de microfibrillas (MFA), son mayores. Un fenómeno a veces relacionado con la JW es la presencia de anillos de crecimiento más amplios y altos niveles de madera de compresión, aunque estas dos últimas relaciones no son mutuamente excluyentes. El año de transición (TY) entre JW y MW se puede encontrar mediante el análisis de todas estas diferentes propiedades que caracterizan a la JW. El límite tiende a cambiar según la propiedad de madera estudiada con patrones variables de la médula a la corteza. Todas estas características tienen efectos indeseables en las propiedades físico-mecánicas y tecnológicas de la madera aserrada para uso estructural. Además, cuanto mayor sea la proporción de JW, mayor incidencia de diferentes distorsiones de secado como el curvado de canto, curvado de cara y alabeo lo que resulta en una disminución en las perspectivas de renta de uso final y retorno económico de los productos aserrados estructurales. Se han dado diferentes nombres a estas dos áreas, las cuales se pueden diferenciar en la dirección transversal del árbol a cualquier altura. También se han expuesto diferentes explicaciones al porqué de dichas variaciones. Si se considera la variación longitudinal, la nomenclatura generalmente empleada es madera interior (CW) y madera exterior (OW). Pero en esta Tesis, utilizaremos la nomenclatura JW/MW, ya que en el sector industrial español es la nomenclatura que se utiliza. Hay varios estudios que evalúan la importancia de la madera juvenil para la madera aserrada estructural en España. Pero no se han realizado muchos estudios sobre las coníferas mediterráneas sobre el efecto de la silvicultura en la cantidad de JW presente en el tronco. La gravedad específica, el MFA y la densitometría se han utilizado ampliamente como indicadores de presencia de JW. En esta Tesis se estudian diferentes metodologías para la determinación de JW en Pinus nigra y Pinus sylvestris con diferente gestión selvícola y esos resultados se comparan con los obtenidos mediante densitometría. Se estudia la influencia de la silvicultura en el TY, en masas de pino laricio y pino silvestre en España, obtenido mediante densitometría. Este análisis se realiza utilizando un modelo mixto lineal segmentado que incluye el análisis de los diferentes efectos, de las covariables incluidas en los diferentes modelos, sobre la densidad. También se estudian las variaciones en el volumen JW y la conicidad de árbol producidas en función de las prácticas selvícolas utilizando la variación radial de densidad de la madera de verano (LW). Otro objetivo de la tesis es la comprobación de si a la altura basal es posible estimar un TY, por medio de la curva de crecimiento acumulado en altura anual y que éste esté relacionado con el obtenido mediante densidad media y de LW anual. Se evalúa la viabilidad de utilizar espectroscopía de infrarrojo cercano (NIR) multipunto, para diferenciar entre JW y MW. Del mismo modo, se evalúa el potencial de las imágenes hiperespectrales de infrarrojo cercano (NIR-HI) para la identificación semiautomática de las áreas de JW y MW en el pino silvestre. Finalmente se estudian los patrones de contracción radial y angular en la dirección transversal a lo largo de diferentes alturas del tronco. En base a los resultados sobre las contracciones, las áreas de JW y MW obtenidas, se relacionaron con las obtenidas a través de la densitometría. Cuando se evalúa el área de JW en un tronco, la micro densitometría de rayos X es un método adecuado para su estudio, los resultados mostraron que la mejor característica de densidad para la automatización del proceso es la densidad de la LW. Si la determinación del TY se realiza mediante datos de cores, que se pueden extraer sobre los árboles en pie, es necesario que la médula necesita esté en el core para evaluar el límite correctamente. La función desarrollada para la realización de los modelos mixtos segmentados proporciona una herramienta potente y más robusta para predecir el TY en un gran número de muestras, en vez de hacerlo individualmente, utilizando perfiles de densidad de LW. El índice de sequía es relevante para el modelado ya que afecta a la densidad de la LW, a la pendiente de la MW o a la determinación del TY. Hasta una altura de 9 metros el TY se produjo antes de la implementación de cualquier tratamiento silvícola, por lo que es necesario hacer otro muestreo en otra masa en la que se hubiesen hecho los tratamientos antes, para evaluar si algún tratamiento pudiera influir o cambiar el TY fuera de la parte del tronco bajo influencia de la copa. Sin embargo, dentro de la copa y en el caso de PN, se demustra que la poda afecta al TY porque la densidad de la LW a la que se alcanza aumenta, retrasando así el TY y aumentando la densidad de la LW. En ambas especies de pino, las claras parecen tener un efecto negativo significativo, aunque pequeño, sobre la densidad de la LW, mientras que los clareos y la poda combinados parecen tener un pequeño efecto positivo en ella, en comparación con el grupo de control. Estos resultados presentados aquí pueden variar dependiendo de la intensidad y el momento de la clara, así como de la cantidad de poda verde llevada a cabo. La respuesta al crecimiento después de los tratamientos silvícolas muestra que la cantidad de JW se reduce en porcentaje, ya que aumenta el volumen total del tronco con cualquier tratamiento selvícola aplicado, para ambas especies, en los bosques puros mediterráneos. El TY calculado utilizando las funciones de crecimiento Chapman-Richards en los incrementos de altura acumulados, no se ajusta a la estimación del TY obtenido a través de la densidad para las procedencias españolas estudiadas de pino silvestre y laricio. Respecto a la calibración entre las mediciones obtenidas con NIR multipunto y los datos de densidad derivados de la micro densitometría de rayos X, ha sido difícil y no se han obtenido resultados lo suficientemente buenos. Por otro lado, el NIR-HI se puede calibrar con los resultados de la micro densitometría de rayos X y la JW, MW y el punto de transición (TP) entre ambos, se puede determinar en la sección transversal del árbol. Los resultados son independientes del tratamiento silvícola aplicado en las plantaciones de pino silvestre estudiadas. El análisis de componentes principales resultó ser una manera útil y fácil de proporcionar información adicional sobre la presencia y ubicación de la madera de compresión. El uso de regresiones de mínimos cuadrados parciales, en nuestro caso, fue la mejor solución para la detección del TP entre JW y MW, cuando la madera de primavera (EW) y la LW se evaluaron por separado. Cada laminilla se clasificó con una diferencia de ±1 anillo en comparación con la obtenida mediante densidad de la LW. Las mayores diferencias fueron de ± 2 de anillos. Una clasificación automática mediante una combinación con una clasificación no supervisada de k-medias anterior entre la EW y la LW, probablemente mejoraría los resultados y podría conducir a una mejor automatización. La contracción radial tiende a ser mayor en los primeros 8 anillos cercanos a la médula, generalmente entre 4 y 9% en los primeros anillos disminuyendo hasta que se estabiliza alrededor del 3%. En cuanto a la contracción angular, es cercana al 0% o incluso negativa cerca de la médula y va aumentando hasta un cierto anillo (9-11), cuando se vuelve más o menos estable alrededor del 2%. Estos resultados son válidos a lo largo del tronco, siendo mayores y la transición producida antes en la contracción radial que angular para cada altura estudiada. No se observan patrones generales a lo largo del mismo árbol en las diferentes alturas muestreadas. La aplicación de los tratamientos silvícolas parece que no tienen ninguna influencia en las variaciones de contracción radial y angular. Si la densidad no es un problema para a clasificación de resistencia de la madera aserrada de uso estructural, el volumen con respecto al área donde la contracción es estable sugiere que, si la contracción longitudinal sigue un patrón similar, el área que podría ser segregada para una mayor calidad es más grande que la proporcionada por la variación radial de densidad de madera de verano

Quantitative wood anatomy

Quantitative wood anatomy analyzes the variability of xylem anatomical features in trees, shrubs, and herbaceous species to address research questions related to plant functioning, growth, and environment. Among the more frequently considered anatomical features are lumen dimensions and wall thickness of conducting cells, fibers, and several ray properties. The structural properties of each xylem anatomical feature are mostly fixed once they are formed, and define to a large extent its functionality, including transport and storage of water, nutrients, sugars, and hormones, and providing mechanical support. The anatomical features can often be localized within an annual growth ring, which allows to establish intra-annual past and present structure-function relationships and its sensitivity to environmental variability. However, there are many methodological challenges to handle when aiming at producing (large) data sets of xylem anatomical data. Here we describe the different steps from wood sample collection to xylem anatomical data, provide guidance and identify pitfalls, and present different image-analysis tools for the quantification of anatomical features, in particular conducting cells. We show that each data production step from sample collection in the field, microslide preparation in the lab, image capturing through an optical microscope and image analysis with specific tools can readily introduce measurement errors between 5 and 30% and more, whereby the magnitude usually increases the smaller the anatomical features. Such measurement errors—if not avoided or corrected—may make it impossible to extract meaningful xylem anatomical data in light of the rather small range of variability in many anatomical features as observed, for example, within time series of individual plants. Following a rigid protocol and quality control as proposed in this paper is thus mandatory to use quantitative data of xylem anatomical features as a powerful source for many research topics

Incorporating 2D tree-ring data in 3D laser scans of coarse-root systems

In times of global change biomass calculations and the carbon cycle is gaining in importance. Forests act as carbon sinks and hence, play a crucial role in worlds and forests carbon budgets. Unfortunately, growth models and biomass calculations existing so far mainly concentrate on the above-ground part of trees. For this reason, the aim of the present study is to develop an annually resolved 3D growth model for tree roots, which allows for reliable biomass calculations and can later be combined with above-ground models. A FARO scan arm was used to measure the surface of a tree-root segment. In addition, ring-width measurements were performed manually on sampled cross sections using WinDENDRO. The main goal of this study is to model root growth on an annual scale by combining these data sets. In particular, a laser scan arm was tested as a device for the realistic reproduction of tree-root architecture, although the first evaluation has been performed for a root segment rather than for an entire root system. Deviations in volume calculations differed between 5% and 7% from the actual volume and varied depending on the used modeling technique. The model with the smallest deviations represented the structure of the root segment in a realistic way and distances and diameter of cross sections were acceptable approximations of the real values. However, the volume calculations varied depending on object complexity, modeling technique and order of modeling steps. In addition, it was possible to merge tree-ring borders as coordinates into the surface model and receive age information in connection with the spatial allocation. The scan arm was evaluated as an innovative and applicable device with high potential for root modeling. Nevertheless, there are still many problems connected with the scanning technique which have an influence on the accuracy of the model but are expected to improve with technical progres

Pith Estimation on Tree Log End Images

International audienceIn this paper, we present an algorithm for pith estimation from digital images of wood cross-sections. The method is based on a probabilistic approach, namely ant colony optimization (ACO). After introducing the approach, we describe the implementation and the reproduction of the method linking to an online demonstration. Results show that the approach performs as well as state-of-the-art methods. The estimated pith is below 5mm from the ground truth. It is a fast method that could be used in real-time environment. This paper also gives the details about the intern parameter choice and shows how to use the C++ source code for testing, as well as provides limit cases of the proposed method and future improvements

Intra-annual to multi-decadal xylem traits in a tropical moist semi-deciduous forest of Central Africa

A witness of a tree’s past conditions is the wood itself. The main research question of this dissertation is how to assess and reveal the driving forces of the patterns of wood traits on pith-to-bark cross-sections in tropical trees. Cambial and leaf phenology was monitored in the Luki Reserve (Mayombe forest, D.R. Congo). Furthermore, X-ray CT densitometry was explored to assess traits in a reliable way, for multiple species. Variability in phenology is observed for T. superba, which requires traits of individual trees to be fixed on a time axis. Furthermore, X-ray CT is a suitable method for assessing traits in a fast way. Cambial activity of understory trees has shown to be species-specific, whilst many trees show zero xylem growth. Finally, 66 years of tree growth was analysed, while trait analysis revealed a median ring count of only 32, thus implying many non-periodical rings. This work presents methodological improvements to measure traits as continuous variables from pith to bark, but also acknowledges that phenology still remains a key aspect in order to fix traits on a time axis. Key words: leaf phenology, wood anatomy, stable isotopes, Mayombe, dendrochronology, X-ray CT densitometr

Automaattinen syväoppimiseen perustuva puun vuosikasvun analysointi sahateollisuudessa

Analysis of wood growth is an important quality control step in a sawmill, as it predicts the structure and load-bearing capabilities of the wood. The annual growth of wood is determined by calculating the distances between the annual rings in a wood end-face. The wood is moving fast in a process line, and manual analysis of woodgrowthisalaborioustaskthatispronetoerrors. Havingtheprocessautomated increases the efficiency and throughput of the sawmill as well as reduces monotonic manual labor, thus providing better working conditions. Automatic counting of annual ring distances has been studied before, however, little research has been done on a sawmill setting which suffers from difficult imaging conditionsandroughwoodend-faceswithvariousdefects. Previousstudieshaveused traditional image processing methods which rely on handcrafted features and fail to generalize well on wood end-faces with varying conditions and arbitrary shaped annual rings. This thesis proposes a general solution to the problem by developing complete end-to-end software for detecting annual rings and analyzing wood growth using deep learning methods. The proposed system is described in detail and compared against traditional computer vision methods. Using data from a real sawmill, the deep learning based approach performs better than the traditional methods.Puun vuosikasvun analysointi on tärkeä osa laadunvarmistusta sahalla, sillä vuosikasvu määrittää puun rakenteen ja kestävyyden. Lankut kulkevat nopeasti tehdaslinjastolla, joten manuaalinen vuosikasvun analysointi on vaivalloista ja virhealtista työtä. Prosessin automatisointi lisää sahan suoritustehoa sekä vapauttaa työntekijän mielekkäämpiin tehtäviin. Puun vuosikasvu määritetään selvittämällä vuosirenkaiden väliset etäisyydet lankun päädystä. Automaattista vuosirenkaiden laskentaa on käsitelty kirjallisuudessa aiemmin, mutta vain muutama tutkimus on tehty sahaympäristössä, jossa kuvausolosuhteet ovat epäotolliset ja puupäädyt ovat karheita ja siistimättömiä. Aiemmat tutkimukset ovat käyttäneet perinteisiä konenäkömenetelmiä, jotka toimivat huonosti vaihtelevan laatuisiin ja muotoisiin puun päätyihin sekä vuosirenkaisiin. Tässä työssä kehitetään automaattinen syväoppimiseen perustuva tietokoneohjelmisto vuosirenkaiden tunnistamiseen ja vuosikasvun analysointiin. Ohjelmisto esitellään läpikotaisesti ja sitä verrataan perinteisiin konenäkömenetelmiin. Vertailussa käytettiin oikealta tehtaalta otettua dataa ja syväoppimiseen perustuva järjestelmä suoriutui perinteisiä menetelmiä paremmin