Litterfall data and hemispherical photos for LAI-calculation on an oak stand at the Intensive Forest Monitoring Station Britz, Brandenburg, 2024 - 2025

Date of acquisition: 2024-07-12 (Leaf on) & 2025-04-16 (Leaf off) Location: Experimental Station Britz, Britz, Brandenburg, Germany DEIMS.iD: https://deims.org/8ee82a9b-5086-4547-b5aa-4064e3314762 Data products: Litterfall: Datafile: litterfall_weight.csv montly sum of leaf weight collected of 13* 0.25m² traps Method after Ukonmaanaho, L., Pitman R, Bastrup-Birk A, Breda N, Rautio P, 2020: Part XIII: Sampling and Analysis of Litterfall. Version 2020-2. In: UNECE ICP Forests Programme Co-ordinating Centre (ed.): Manual on methods and criteria for harmonized sampling, assessment, monitoring and analysis of the effects of air pollution on forests. Thünen Institute for Forests Ecosystems, Eberswalde, Germany, 18 p. + Annex [https://www.icp-forests.net/monitoring-and-research/icp-forests-manual]. Solariscope data subplot_id: 1-5 subplots Date: Date of measurement Name: Numbered name of photo & threshold Timestamp: Time of measurement DSF: Direct Site Factor ISF: Indirect Site Factor TSF: Total Site Factor Opn: Openness GapF: Gap Fraction LAI: Leaf Area Index bestthreshold: T = manual best choice of threshold to binarise between plant and sky Datafile: solariscope_data.csv Folder: rawimages: raw images used for internal processing Folder: images: processed images with 3 thresholds per subplot used for manual choice of best threshold to binarise between plant and sky Hemispherical photos date: Date of measurement time: Time of measurement cloudfraction: Cloudfraction in 1/8 steps; 8/8 means completly cloudy ev: exposure value correction of series -1,-2,-3 subplot: 1-5 subplots photonr: Numbered name of photo bestchoice: manual best choice of phot of exposure series, minimum of overexposure, maximum of exposure range Canon EOS REBEL T1i and a 5.6 mm 185° fisheye objective by Sunex, automatically horizontal levelled by an o-mount by Regent Instruments Inc., lens height above the floor is 1.3 meter red light indicates north Format: compressed: jpg and canon raw-format: cr2 Meta-Datafile hemispherical_photo.csv Folder: hemispherical_photos R-Scripts: To run the hemispherical photo processing and produce LAI results: from the repository rootRscript pcm_study_britz_hemi_photos/2025-11-26-hemispherical_photos_2_lai.R To compute LAI from litterfall and Solariscope ground-truth data: Rscript pcm_study_britz_hemi_photos/2025-11-24-litterfall2LAI.RRscript pcm_study_britz_hemi_photos/2025-11-24-solariscope2LAI.R Note: The scripts assume the repository root is the current working directory and use paths relative to the repo. If you run from elsewhere, adjust paths accordingly. output/` - Script outputs and derived visualizations: - `*_binarize_fisheye_*.png` - Binarized images generated by `binarize_fisheye()` for manual QA. - `*_gapfrac_fisheye_*.png` - Gap-fraction plots by zenith ring. - `_violine_plot_*` - Violin plots of LAI distributions by subplot or EV. - `binary_overlay_*.jpg` - Overlays between original and binary classification. - `results_LAI_from_hemispherical_photos.RData` - R data file with consolidated LAI results and objects. - `results_LAI_from_hemispherical_photos.csv` - CSV summary table with LAI metrics for each image.采集日期：2024-07-12（展叶期）与2025-04-16（落叶期） 地点：德国勃兰登堡州布里茨实验站（Experimental Station Britz, Britz, Brandenburg, Germany） DEIMS 标识符：https://deims.org/8ee82a9b-5086-4547-b5aa-4064e3314762 数据产品： 一、凋落物收集数据 数据文件：litterfall_weight.csv，包含13个0.25㎡采样器收集的叶片重量月度总和。采样方法参照Ukonmaanaho L、Pitman R、Bastrup-Birk A等（2020）发布的《第十三部分：凋落物采样与分析》（2020-2版），收录于联合国欧洲经济委员会ICP森林（UNECE ICP Forests）项目协调中心主编：《空气污染对森林影响的标准化采样、评估、监测与分析方法和标准手册》，德国埃伯斯瓦尔德图能森林生态系统研究所（Thünen Institute for Forests Ecosystems），共18页及附录[https://www.icp-forests.net/monitoring-and-research/icp-forests-manual]。 二、Solariscope 监测数据 子样地ID：1-5号子样地 测量日期（Date）：测量的具体日期 照片与阈值编号名称（Name）：照片及阈值的编号标识 测量时间戳（Timestamp）：测量的时间点 直接立地因子（Direct Site Factor, DSF）、间接立地因子（Indirect Site Factor, ISF）、总立地因子（Total Site Factor, TSF）、开阔度（Openness, Opn）、间隙率（Gap Fraction, GapF）、叶面积指数（Leaf Area Index, LAI） 最佳阈值（bestthreshold）：用于区分植物与天空的手动选定最优二值化阈值 数据文件：solariscope_data.csv 附属文件夹： - rawimages：用于内部处理的原始图像文件 - images：每个子样地包含3种阈值的处理后图像，用于手动选择最优二值化阈值 三、半球摄影数据 测量日期（date）：拍摄日期 测量时间（time）：拍摄时间 云量分数（cloudfraction）：以1/8为等级的云量占比，8/8表示完全阴天 曝光值修正（ev）：序列曝光的曝光值修正量，取值为-1、-2、-3 子样地（subplot）：1-5号子样地 照片编号（photonr）：照片的编号名称 最佳选择（bestchoice）：曝光序列中手动选定的最优照片，即过曝程度最低且处于曝光范围上限的照片 拍摄设备：佳能EOS REBEL T1i相机搭配Sunex公司5.6 mm 185°鱼眼镜头，通过Regent Instruments Inc.生产的O型支架自动实现水平校准，镜头距地面高度为1.3米。红光指示正北方向。 图像格式：压缩格式为JPEG，佳能原始格式为CR2 元数据文件：hemispherical_photo.csv 附属文件夹：hemispherical_photos 四、R脚本说明 1. 半球照片处理与叶面积指数生成脚本：从代码仓库根目录执行以下命令： `Rscript pcm_study_britz_hemi_photos/2025-11-26-hemispherical_photos_2_lai.R` 2. 基于凋落物与Solariscope实测数据计算叶面积指数的脚本： `Rscript pcm_study_britz_hemi_photos/2025-11-24-litterfall2LAI.R` `Rscript pcm_study_britz_hemi_photos/2025-11-24-solariscope2LAI.R` 注意：脚本默认以代码仓库根目录为当前工作目录，并使用相对路径。若在其他路径运行，请相应调整路径。 五、输出目录（output/） 脚本输出结果与衍生可视化内容包括： - `*_binarize_fisheye_*.png`：由`binarize_fisheye()`函数生成的二值化图像，用于手动质量核查 - `*_gapfrac_fisheye_*.png`：按天顶环划分的间隙率绘图 - `_violine_plot_*`：按子样地或曝光值（Exposure Value, EV）划分的叶面积指数分布小提琴图 - `binary_overlay_*.jpg`：原始图像与二值分类结果的叠加图 - `results_LAI_from_hemispherical_photos.RData`：包含整合后的叶面积指数结果与对象的R数据文件 - `results_LAI_from_hemispherical_photos.csv`：包含每张照片叶面积指数指标的CSV汇总表