无人机高光谱影像与冠层树种多样性监测

冠层树种多样性是自然森林生态系统功能和服务的重要基础。及时掌握冠层多样性的现状及变化趋势, 是探讨诸多重要生态学问题的前提, 更是制定合理生物多样性保护策略的基础。但受制于传统的多样性信息采集方法, 区域尺度的高精度冠层多样性监测发展较为缓慢; 许多在气候变化和人类干扰下的生物多样性分布信息得不到及时更新。近年来基于无人机的冠层高光谱影像收集与分析技术的发展, 使得冠层多样性监测迎来了新的发展契机。本文从森林冠层高光谱影像出发, 介绍了与多样性监测相关的无人机航拍和基于深度学习的图像处理技术, 并结合已有文献, 探讨了无人机高光谱应用于森林冠层树种多样性监测的研究现状、可行性、优势及缺陷等。我们认为冠层高光谱影像为多样性监测提供了不可或缺且丰富的原始信息; 而无人机与高光谱相机的结合, 使得区域化高频率(如每周)、高精度(如分米乃至厘米级)的冠层多样性信息自动化收集成为可能。然而高光谱影像数据量大、数据维度高与数据结构非线性的特点为影像处理带来了挑战, 而深度学习技术的飞跃, 使得从冠层高光谱影像中提取个体及物种信息达到了极高精度。恰当地使用这些技术将大大提升冠层树种多样性的自动化监测水平, 由此也将帮助我们在当前剧变环境下及时掌握森林冠层多样性的现状与变化, 为生物多样性研究与保护提供可靠的数据支撑。     

Variation in performance of the tree fern Cyathea caracasana (Cyatheaceae) across a successional mosaic in an Andean cloud forest

In Andean forests, Cyathea caracasana grows across a range of successional habitats. This study documents variation in several measures of plant performance (stem growth, leaf production, leaf longevity, and spore production) in C. caracasana growing in open habitat, low-canopy secondary forest, and high-canopy secondary forest, based on 33 mo of observation. In open habitat, C. caracasana displayed significantly higher growth rates, leaf production rates, and leaf turnover than in either of the forested habitats. The highest rates of spore production were also observed in open-habitat individuals, with only one plant in the forest understory producing spores during the study. Despite low growth and no reproduction, I observed no mortality among ferns in the forest understory. These data show that C. caracasana performs best under conditions of full sun but can persist under the closed canopy. This suggests a life history in which periods of rapid growth, spore production, and recruitment in forest gaps alternate with low growth rate and persistence in the understory. A phylogenetic perspective suggests that the habitat flexibility, which might conventionally mark C. caracasana as a habitat generalist, is better interpreted as specialization for the dynamic forest in which it grows.     

Vertical stratification of ichneumonid wasp communities: the effects of forest structure and life‐history traits

Parasitoid wasp communities of the canopy of temperate forests are still largely unexplored. Very little is known about the community composition of parasitoids between canopy and understory and how much of this difference is related to forest structure or parasitoid biological strategies. In this study we investigated upon the difference in the community composition of the parasitic wasps Ichneumonidae between canopy and understory in a lowland temperate forest in northern Italy. We used general linear models to test whether parasitic strategy modifies species vertical stratification and the effect of forest structure. We also tested differences in β‐diversity between canopy and understory traps and over time within single forest layers. We found that stand basal area was positively related to species richness, suggesting that the presence of mature trees can influence local wasp diversity, providing a higher number of microhabitats and hosts. The ichneumonid community of the canopy was different from that of the understory, and the β‐diversity analysis showed higher values for the canopy, due to a higher degree of species turnover between traps. In our analyses, the vertical stratification was different between groups of ichneumonids sharing different parasitic strategies. Idiobiont parasitoids of weakly or deeply concealed hosts were more diverse in the understory than in the canopy while parasitoids of spiders were equally distributed between the two layers. Even though the ichneumonid community was not particularly species‐rich in the canopy of the temperate forests, the extension of sampling to that habitat significantly increased the number of species recorded.     

Canopy bird assemblages are less influenced by habitat age and isolation than understory bird assemblages in Neotropical secondary forest

Secondary forest habitats are increasingly recognized for their potential to conserve biodiversity in the tropics. However, the development of faunal assemblages in secondary forest systems varies according to habitat quality and species‐specific traits. In this study, we predicted that the recovery of bird assemblages is dependent on secondary forest age and level of isolation, the forest stratum examined, and the species’ traits of feeding guild and body mass. This study was undertaken in secondary forests in central Panama; spanning a chronosequence of 60‐, 90‐, and 120‐year‐old forests, and in neighboring old‐growth forest. To give equal attention to all forest strata, we employed a novel method that paired simultaneous surveys in canopy and understory. This survey method provides a more nuanced picture than ground‐based studies, which are biased toward understory assemblages. Bird reassembly varied according to both habitat age and isolation, although it was challenging to separate these effects, as the older sites were also more isolated than the younger sites. In combination, habitat age and isolation impacted understory birds more than canopy‐dwelling birds. Proportions of dietary guilds did not vary with habitat age, but were significantly different between strata. Body mass distributions were similar across forest ages for small‐bodied birds, but older forest supported more large‐bodied birds, probably due to control of poaching at these sites. Canopy assemblages were characterized by higher species richness, and greater variation in both dietary breadth and body mass, relative to understory assemblages. The results highlight that secondary forests may offer critical refugia for many bird species, particularly specialist canopy‐dwellers. However, understory bird species may be less able to adapt to novel and isolated habitats and should be the focus of conservation efforts encouraging bird colonization of secondary forests.     

西双版纳热带雨林林窗空间分布格局及其特征数与林窗下植物多样性的相关性

林窗作为森林群落中一种重要的干扰方式, 对林下物种构成有着重要的影响。开展林窗空间格局及其特征指数与林下植物多样性关系研究对于探讨林窗对林下生物多样性的影响有重要意义, 有助于进一步了解群落动态, 在物种多样性保护方面也具有指导作用。本研究在西双版纳热带雨林地区随机选取3块大小为1 ha的热带雨林为研究样地, 采用轻小型六旋翼无人机搭载Sony ILCE-A7r可见光传感器, 分别获取各个样地的高清数字影像, 结合数字表面高程模型以及各个样地的地形数据用以确定各样区的林窗分布格局, 并进一步提取出各林窗的景观格局指数。结合地面样方基础调查数据, 对各样地各林窗下植物多样性情况进行统计, 旨在分析热带雨林林窗空间分布格局以及林窗下植物多样性对各林窗空间格局特征的响应情况。研究表明, 西双版纳州热带雨林林窗呈大而分散的空间分布, 林窗空间格局特征指数如林窗形状复杂性指数、林窗面积都与林下植物多样性呈显著正相关关系。在面积小的林窗下, 较之林窗形状复杂性因子, 林窗面积大小对林下植物多样性影响更显著; 在面积达到一定程度后, 相对于面积因子, 林窗形状复杂性指数对林下植物多样性影响更显著, 各样地林窗皆趋于向各自所处样地顶极群落发展。     

间伐对杨桦次生林冠层结构及林下光照的影响

自然或人为干扰产生的森林冠层结构和林下光照差异是造成林下环境异质性、物种多样性的主要原因,对森林生态系统的结构、过程与格局具有重要作用.以桃山林场2块50 m×50 m的杨桦次生林固定样地为研究对象,分别作为间伐和对照样地,于2012—2016年、2018年获取样地冠层影像,通过方差分析、马尔科夫模型等方法分析其冠层结构、林下光照动态及间伐后林冠的恢复规律.结果表明: 间伐措施能显著调整冠层结构和林下光照,并能持续较长的作用时间,但调整效果随时间逐渐降低;间伐后冠层结构及林下光照的变化速度随时间推移而降低,间伐后前3年林冠恢复速度较快,3年后恢复速度降低并趋于平缓;林下光照与林冠开度呈显著正相关,与叶面积指数呈显著负相关,其中林下散射辐射与冠层结构参数的相关性最大,且间伐样地冠层结构与林下光照的相关性大于对照样地;间伐后冠层的恢复速度与林冠开度大小有关,林冠开度越大,林冠恢复越快,向更小林冠开度转移的时间越早.马尔科夫模型能够模拟冠层结构分布的变化,可用来预测冠层结构动态.     

白云山国家森林公园不同人为干扰强度的群落冠层结构和光照特征

为探究森林冠层结构与林下光照的变化规律及其相关性,在河南省白云山国家森林公园选取人工林、择伐林、皆伐林和老龄林建立四块面积为1 hm²（100 m×100 m）的固定监测样地,利用半球面影像技术获取冠层结构及林下光照数据。研究发现：1）随着人为干扰强度降低,冠层覆盖度与叶面积指数呈增加趋势,林下散射辐射与直接辐射呈减少趋势;2）择伐林冠层覆盖度与叶面积指数最大,平均叶倾角与透光比最小,林下光照（直接辐射、散射辐射）与冠层覆盖度和叶面积指数都呈显著负相关,林下散射辐射与冠层覆盖度和叶面积指数的负相关关系最强;3）处于不同干扰强度的群落由于冠层结构的差异,形成了不同群落内特定的光照环境。研究结果丰富了暖温带-亚热带生态过渡区森林冠层结构与林下光照动态变化研究资料,同时也为该区域森林的恢复与重建等提供科学的依据。     

西双版纳热带雨林干季林冠层雾露形成的小气候特征研究

对西双版纳热带雨林干季林冠层雾露形成的小气候特征进行了观测研究。结果表明,雾露首先形成于最上林冠层,林下露水的形成迟于林上3～4h,林下雾是由上层雾变浓、下沉而来。夜间,雾形成前,气温高于叶表温;雾形成后,气温则低于叶表温,且气温及叶表温均有回升。雾露的形成不仅凝结了水汽进入森林,同时也对森林起到了一定的保温作用,这对热带雨林的生存和发展具有致关重要的作用。     

The application of convolution neural network based cell segmentation during cryopreservation

For most of the cells, water permeability and plasma membrane properties play a vital role in the optimal protocol for successful cryopreservation. Measuring the water permeability of cells during subzero temperature is essential. So far, there is no perfect segmentation technique to be used for the image processing task on subzero temperature accurately. The ice formation and variable background during freezing posed a significant challenge for most of the conventional segmentation algorithms. Thus, a robust and accurate segmentation approach that can accurately extract cells from extracellular ice that surrounding the cell boundary is needed. Therefore, we propose a convolutional neural network (CNN) architecture similar to U-Net but differs from those conventionally used in computer vision to extract all the cell boundaries as they shrank in the engulfing ice. The images used was obtained from the cryo-stage microscope, and the data was validated using the Hausdorff distance, means ± standard deviation for different methods of segmentation result using the CNN model. The experimental results prove that the typical CNN model extracts cell borders contour from the background in its subzero state more coherent and effective as compared to other traditional segmentation approaches.     

海南岛热带天然针叶林主要树种的空间格局及关联性

天然针叶林在热带地区虽较为少见, 但其对维持热带地区的生物多样性和生境异质性具有特殊意义。在我国热带天然针叶林集中分布面积最大的海南霸王岭林区, 作者选择伴生阔叶树种优势度不同的两种典型南亚松(Pinus latteri)天然林(简称纯林和混交林), 采用点格局法分析了其林冠层、亚林层和林下层主要树种的空间分布格局及其关联性。结果表明: (1)纯林中林冠层的南亚松主要为聚集分布, 混交林中在较小尺度上为聚集分布, 在较大尺度上为随机分布。(2)纯林中亚林层树种在较小尺度上为聚集分布, 在较大尺度上为随机分布, 在混交林中主要为聚集分布。(3)纯林中林下层树种主要呈现为随机分布, 而在混交林中主要为聚集分布。(4)随着尺度的增加, 林冠层与其他两个层次的树种, 在纯林中表现出从空间无关联到正关联的变化趋势, 而在混交林中则表现出从空间无关联到负关联的变化趋势。(5)亚林层与林下层树种在各个尺度上都表现为空间正关联。由此可见, 热带天然针叶林中优势种南亚松对伴生阔叶树种的分布格局具有重要影响。     

RootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues

The morphology of plant root anatomical features is a key factor in effective water and nutrient uptake. Existing techniques for phenotyping root anatomical traits are often based on manual or semi-automatic segmentation and annotation of microscopic images of root cross sections. In this article, we propose a fully automated tool, hereinafter referred to as RootAnalyzer, for efficiently extracting and analyzing anatomical traits from root-cross section images. Using a range of image processing techniques such as local thresholding and nearest neighbor identification, RootAnalyzer segments the plant root from the image’s background, classifies and characterizes the cortex, stele, endodermis and epidermis, and subsequently produces statistics about the morphological properties of the root cells and tissues. We use RootAnalyzer to analyze 15 images of wheat plants and one maize plant image and evaluate its performance against manually-obtained ground truth data. The comparison shows that RootAnalyzer can fully characterize most root tissue regions with over 90% accuracy.     

Budburst and leaf area expansion measured with a novel mobile camera system and simple color thresholding

Plant phenology relates strongly to primary productivity and the energy that enters into ecological food webs, and thus is vital in understanding ecosystem function and the effects of climate and climate change. The manual collection of phenological data is labor-intensive and not easily scalable, thus the ability to quantify leaf flush and other parameters at many locations requires innovative new methodologies such as the use of visible light digital cameras. Improved imaging performance was obtained by using a cabled, mobile camera system that allowed a repeated image census of branches of Rhododendron occidentale in the understory along a 30 m transect during leaf flush. Automatic division of acquired images into areas of interest (leaves) and background for calculating leaf area was accomplished by thresholding images in different color spaces. Transformation of the color space into the hue, saturation, and luminance (HSL) color space before thresholding resulted in a mean RMS error of 21.2 cm² compared to hand-counts of leaf area. Thresholding in the native red, green, and blue (RGB) color space to isolate leaves resulted in a larger error, as did using algebraic combinations of the color components or color ratios. Relating physiological function to images, as for sap flow for branches of R. occidentale, indicates that the greening and calculated leaf area of a species as detected by imagers requires additional meteorological sensor data for interpretation.     

A method of calculating phenotypic traits for soybean canopies based on three-dimensional point cloud

Analysis of soybean phenotypes is a core motivation behind soybean breeding. However, amounts of manual measures are required in obtaining canopy phenotypic traits via traditional methods. Moreover, deficiencies such as time consumption, strong subjectivity, and inaccuracy can be also detected in manual measurement. In order to achieve automatic extraction of phenotypic traits in the research of soybean breeding, a method of acquiring soybean phenotypic traits was proposed on the basis of a Kinect sensor with three soybean varieties (incl. KANGXIAN9, KANGXIAN13, and FUDOU6) as research objects, implementing the calculation of plant height (PH), leaf area index (LAI). Firstly, the canopy image information was acquired vertically to extract canopy data with the registration of color images and depth point cloud data. Secondly, a soybean single plant was segmented from the group canopy using the bounding box method; also, the height of the soybean plant was solved using the distance information; meanwhile, the canopy LAI was calculated with extinction coefficients that were optimized by the beer-lambert law. According to experimental results, determination coefficients R² of the calculated value and the measured value of the plant height and the leaf area index of the three soybean varieties are greater than 0.94. It can be seen that calculated results can meet the accuracy requirement of phenotypic traits in soybean breeding.     

Thermal adaptation and diversity in tropical ecosystems: evidence from cicadas (Hemiptera, Cicadidae)

The latitudinal gradient in species diversity is a central problem in ecology. Expeditions covering approximately 16°54' of longitude and 21°4' of latitude and eight Argentine phytogeographic regions provided thermal adaptation data for 64 species of cicadas. We test whether species diversity relates to the diversity of thermal environments within a habitat. There are general patterns of the thermal response values decreasing in cooler floristic provinces and decreasing maximum potential temperature within a habitat except in tropical forest ecosystems. Vertical stratification of the plant communities leads to stratification in species using specific layers of the habitat. There is a decrease in thermal tolerances in species from the understory communities in comparison to middle level or canopy fauna. The understory Herrera umbraphila Sanborn & Heath is the first diurnally active cicada identified as a thermoconforming species. The body temperature for activity in H. umbraphila is less than and significantly different from active body temperatures of all other studied species regardless of habitat affiliation. These data suggest that variability in thermal niches within the heterogeneous plant community of the tropical forest environments permits species diversification as species adapt their physiology to function more efficiently at temperatures different from their potential competitors.     

Segmentation of Fluorescence Microscopy Images for Quantitative Analysis of Cell Nuclear Architecture

Considerable advances in microscopy, biophysics, and cell biology have provided a wealth of imaging data describing the functional organization of the cell nucleus. Until recently, cell nuclear architecture has largely been assessed by subjective visual inspection of fluorescently labeled components imaged by the optical microscope. This approach is inadequate to fully quantify spatial associations, especially when the patterns are indistinct, irregular, or highly punctate. Accurate image processing techniques as well as statistical and computational tools are thus necessary to interpret this data if meaningful spatial-function relationships are to be established. Here, we have developed a thresholding algorithm, stable count thresholding (SCT), to segment nuclear compartments in confocal laser scanning microscopy image stacks to facilitate objective and quantitative analysis of the three-dimensional organization of these objects using formal statistical methods. We validate the efficacy and performance of the SCT algorithm using real images of immunofluorescently stained nuclear compartments and fluorescent beads as well as simulated images. In all three cases, the SCT algorithm delivers a segmentation that is far better than standard thresholding methods, and more importantly, is comparable to manual thresholding results. By applying the SCT algorithm and statistical analysis, we quantify the spatial configuration of promyelocytic leukemia nuclear bodies with respect to irregular-shaped SC35 domains. We show that the compartments are closer than expected under a null model for their spatial point distribution, and furthermore that their spatial association varies according to cell state. The methods reported are general and can readily be applied to quantify the spatial interactions of other nuclear compartments.     

Bird community responses to disturbance in a forestry concession in lowland Bolivia

Bird community characteristics of three sites with different levels of disturbance were studied using transect surveys during the dry season in a subtropical humid forest in Bolivia. One area had been unintentionally burned 4 years prior and selectively harvested (DIS) 1 year prior to sampling. A second area had been selectively harvested 1 year prior to sampling and had no recent history of fire (HAR). Species richness, as assessed by species–time curves and rarefaction, was higher in both altered areas than in undisturbed forest (INT). In general, frugivores and omnivores were more abundant in both altered areas compared to intact forest. Canopy frugivores, understory omnivores and multiple-strata omnivores were most abundant in HAR. Canopy frugivores, near-ground insectivores, understory and multiple-strata omnivores were least abundant in INT, although INT had the highest abundances of canopy insectivores and near-ground omnivores. Richness and abundance of widespread species with low habitat specificity was higher in both areas that experienced disturbance compared to intact forest. Differences in bird community structure between disturbed and intact forest at this site are attributed primarily to the addition of widespread species with less narrow habitat requirements, and possibly to changes in the distribution of different food types.     

Cultivation of Non‐timber Forest Products Alters Understory Light Availability in a Humid Tropical Forest in Mexico1

The planting of non‐timber forest products (NTFPs) in the understory of tropical forests is promoted in many regions as a strategy to conserve forested lands and meet the economic needs of rural communities. While the forest canopy is left intact in most understory plantations, much of the midstory and understory vegetation is removed in order to increase light availability for cultivated species. We assessed the extent to which the removal of vegetation in understory plantations of Chamaedorea hooperiana Hodel (Arecaceae) alters understory light conditions. We also examined how any changes in light availability may be reflected by changes in the composition of canopy tree seedlings regenerating in understory plantations. We employed a blocked design consisting of four C. hooperiana plantation sites; each site was paired with an adjacent, unmanaged forest site. Hemispherical canopy photographs were taken and canopy tree seedlings were identified and measured within 12 3 × 2 m randomly placed plots in each site for a total of 96 plots (4 blocks × 2 sites × 12 plots). Plantation management did not affect canopy openness or direct light availability but understory plantations had a higher frequency of plots with greater total and diffuse light availability than unmanaged forest. Comparisons of canopy tree seedling composition between understory plantations and unmanaged forest sites were less conclusive but suggest that management practices have the potential to increase the proportion of shade‐intolerant species of tree seedlings establishing in plantations. Given the importance of advanced regeneration in gap‐phase forest dynamics, these changes may have implications for future patterns of succession in the areas of forest where NTFPs are cultivated.     

Spatial and seasonal patterns of microsite light availability in a remnant fragment of deciduous riparian forest and their implication in the conservation ofArisaema heterophyllum, a threatened plant species

Seasonal and spatial patterns of light availability were investigated in the understory of a small fragment (approximately 1300 m²) of a riparian deciduous forest of the Kokai River in central Japan dominated byQuercus acutissima Carruth., with the aim to understand the characteristics of microsite light availability forArisaema heterophyllum Blume, a threatened plant species uniquely associated with the riparian habitat. Diffuse site factor, which is the ratio of PFD (photon flux density, 400–700 nm) at a microsite to the open sky reference under diffuse light condition, was shown to be a satisfactory index for the evaluation of light availability for the understory plants in the habitat. Diffuse site factor 1,0 1,000 understory microsites along a 20 m transect from the edge to the interior of the forest, showed conspicuous seasonal changes in both mean and variation. Light availability decreased with seasonal tree canopy regeneration, with the highest spatial heterogeneity being recorded during the time of canopy closure. Auto-correlations of microsite light availability between different seasons were considerably high, suggesting the stability of relative light availability for individual microsites throughout the growing season ofA. heterophyllum. Fairly high light availability during summer season, which surpassed 20% of the open sky reference in most microsites, would be important for the growth and persistence of summer herbaceous plants likeA. heterophyllum.     

Saplings distribution in relation to topography and canopy openness in an evergreen broad-leaved forest

We examined the spatial distribution of saplings in relation to topography and stand structure in a subtropical evergreen broad-leaved forest in the northern part of Okinawa Island, Japan. The distributions of most species were influenced mainly by topography but also by canopy openness. Species were arranged along a topographical gradient from concave areas with low canopy openness to convex areas with high canopy openness. Canopy species were arranged along a gradient from unstable fertile areas to stable infertile areas. Species occurring mostly in convex areas had a narrower distribution range than those in concave sites. Thus, habitat heterogeneity provided by topography and stand structure appears to be important factors for maintaining high species diversity in the understory of this subtropical evergreen broad-leaved forest.