DOI: 10.5281/zenodo.3780391
title: Technical method comparison of leaf area assessments from leaves scanned with a flatbed scanner.

description: <b>Description: </b>Leaf scans were used for a technical comparison of different programs calculating leaf area. For this approach, a subset of leaf scans was compiled from trees in selectively logged forest at SAFE and in old-growth forest in Danum Valley and Maliau Basin, sampled during the BALI project traits campaign. Leaf area determination is compared for five different methods and twp groups of leaves: "easy" (mostly simple leaves and small to medium sized leaves that result in comparibly easy scans to analyse) and "tough" (usually big and compound leaves that lead to challenging scans with shadows). For the purpose of a methods comparison, leaf areas are not summed up per leaf or tree level but instead provided on the basis of each individual scan image.<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>Biodiversity and land-use impacts on tropical ecosystem function (BALI): Quantifying functional trait distributions across the disturbance gradient</b><b>Funding: </b>These data were collected as part of research funded by: NERC (Standard grant, NE/K016253/1)This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.<b>Permits: </b>These data were collected under permit from the following authorities:Sabah Biodiversity Centre (Research licence JKM/MBS.1000-2.2(385))<b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This dataset consists of 3 files: Both_leaf_area_scans_18062020.xlsx, tough.zip, easy.zip<b>Both_leaf_area_scans_18062020.xlsx</b>This file contains dataset metadata and 2 data tables:<b>Scan_level_data</b> (described in worksheet Scan_level_data)Description: Area measurements of each individual scanNumber of fields: 16Number of data rows: 3507Fields: <b>location</b>: Location (Field type: categorical)<b>forest_type</b>: Forest type: OG: old-growth plots, Maliau and Danum; SL: selectively logged plots at SAFE (Field type: categorical)<b>forestplots_name</b>: Plot name coherent with forestplots database (Field type: id)<b>plot_name_trait_campaign</b>: Plot name used during the BALI trait campaign (Field type: id)<b>sample_code</b>: Sample code referencing: plot-'T'(ree) ID-branch type (Field type: id)<b>branch_type</b>: Binary classification of branch sampled depending on their position in the tree crown. BS: sun branch; BSH: shade branch (Field type: id)<b>sampling_date</b>: Date of sampling (Field type: date)<b>tree_id</b>: Reference for tree tag label (Field type: id)<b>species</b>: Tree species (Field type: taxa)<b>dataset</b>: Data set: easy: leaves selected at random from the total dataset that have undergone manual processing and editing to improve the image quality; tough: images that were selected on the basis of their features, these included images with dark shadows, low contrast, multiple leaf fragments, or strongly three-dimensional leaves. (Field type: id)<b>resolution_DPI</b>: Resolution of image in dpi (dots per inch), scanner resolution (Field type: numeric)<b>filename</b>: Filename of scanner image: see dataset field for the appropriate zipfile. (Field type: id)<b>branch_code</b>: Branch code referring to the collection of sample, usually one branch was used for the entire sample collection (1), in some cases several branches were collected to gather sufficient plant material. The number is reflected in the sample code but has little relevance for the sample itself (Field type: id)<b>leaf_code</b>: Number of leaf (Field type: replicate)<b>leaf_part</b>: Classifying the part of the leaf on scanned image: Single: single leaf with petiole; C1: one leaflet of a compound leaf; C2: all remaining parts of compound leaf excluding the leaflet scanned for C1 (Field type: id)<b>leaf_chunk_code</b>: Number of scans per individual leaf sample (Field type: id)<b>Leaf_level_data</b> (described in worksheet Leaf_level_data)Description: Leaf area measurements combined for each individual leaf, which may be added up from several scansNumber of fields: 20Number of data rows: 1087Fields: <b>location</b>: Location (Field type: categorical)<b>forest_type</b>: Forest type: OG: old-growth plots, Maliau and Danum; SL: selectively logged plots at SAFE (Field type: categorical)<b>forestplots_name</b>: Plot name coherent with forestplots database (Field type: id)<b>plot_name_trait_campaign</b>: Plot name used during the BALI trait campaign (Field type: id)<b>sample_code</b>: Sample code referencing: plot-'T'(ree) ID-branch type-leaf replicate or plot-'G'(ap individual) ID-branch type-leaf replicate (Field type: id)<b>tree_id</b>: Reference for tree tag label (Field type: id)<b>branch_code</b>: Branch code referring to the collection of sample, usually one branch was used for the entire sample collection (1), in some cases several branches were collected to gather sufficient plant material. The number is reflected in the sample code but has little relevance for the sample itself (Field type: id)<b>branch_type</b>: Binary classification of branch sampled depending on their position in the tree crown. BS: sun branch; BSH: shade branch (Field type: id)<b>leaf_code</b>: Number of leaf (Field type: replicate)<b>dataset</b>: Data set: easy: leaves selected at random from the total dataset that have undergone manual processing and editing to improve the image quality; tough: images that were selected on the basis of their features, these included images with dark shadows, low contrast, multiple leaf fragments, or strongly three-dimensional leaves. (Field type: id)<b>resolution_DPI</b>: Resolution of image in dpi (dots per inch), scanner resolution (Field type: numeric)<b>leaf_area_manual_(cm^2)</b>: Leaf area determined manually in imageJ (Field type: id)<b>leaf_area_BS_(cm^2)</b>: Leaf area determined automatically in Blackspot (Field type: id)<b>leaf_area_ELA_(cm^2)</b>: Leaf area determined automatically in Easy Leaf Area (Field type: id)<b>leaf_area_LeafCalc_(cm^2)</b>: Leaf area determined automatically in LeafCalc (Field type: id)<b>leaf_area_LA_(cm^2)</b>: Leaf area determined automatically in R package Leaf Area (Field type: id)<b>number_leaf_chunks_BS</b>: Number of leaf chunks counted in Blackspot (Field type: id)<b>number_leaf_chunks_ELA</b>: Number of leaf chunks counted in Easy Leaf Area (Field type: id)<b>number_leaf_chunks_LeafCalc</b>: Number of leaf chunks counted in LeafCalc (Field type: id)<b>number_leaf_chunks_LA</b>: Number of leaf chunks counted in R package Leaf Area (Field type: id)<b>tough.zip</b>Description: ZIP file containing images (leaf scans) used by the method comparison<b>easy.zip</b>Description: ZIP file containing images (leaf scans) used by the method comparison<b>Date range: </b>2014-05-01 to 2018-09-01<b>Latitudinal extent: </b>4.5000 to 5.0700<b>Longitudinal extent: </b>116.7500 to 117.8200<b>Taxonomic coverage: </b><br> All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets. - Plantae <br> - - Tracheophyta <br> - - - Magnoliopsida <br> - - - - Rosales <br> - - - - - Moraceae <br> - - - - - - <i>Antiaris</i> <br> - - - - - - - <i>Antiaris toxicaria</i> <br> - - - - - - <i>Artocarpus</i> <br> - - - - - - - <i>Artocarpus anisophyllus</i> <br> - - - - - - - <i>Artocarpus glaucus</i> <br> - - - - - - - <i>Artocarpus integer</i> <br> - - - - - - - <i>Artocarpus odoratissimus</i> <br> - - - - - - - <i>Artocarpus tamaran</i> <br> - - - - - - <i>Ficus</i> <br> - - - - - - - <i>Ficus hispida</i> <br> - - - - - - - <i>Ficus septica</i> <br> - - - - - - - <i>Ficus uncinata</i> <br> - - - - - - - <i>Ficus variegata</i> <br> - - - - - Cannabaceae <br> - - - - - - <i>Gironniera</i> <br> - - - - - - - <i>Gironniera nervosa</i> <br> - - - - - - <i>Trema</i> <br> - - - - - - - <i>Trema orientalis</i> <br> - - - - - Rosaceae <br> - - - - - - <i>Prunus</i> <br> - - - - - - - <i>Prunus javanica</i> <br> - - - - - - <i>Pygeum</i> <br> - - - - - - - <i>Pygeum beccarii</i> (as synonym: <i>Prunus beccarii</i>)<br> - - - - - Urticaceae <br> - - - - - - <i>Dendrocnide</i> <br> - - - - - - - <i>Dendrocnide elliptica</i> <br> - - - - Lamiales <br> - - - - - Oleaceae <br> - - - - - - <i>Chionanthus</i> <br> - - - - - - - <i>Chionanthus macrocarpus</i> <br> - - - - - - - <i>Chionanthus pluriflorus</i> <br> - - - - - Lamiaceae <br> - - - - - - <i>Callicarpa</i> <br> - - - - - - - <i>Callicarpa pentandra</i> <br> - - - - Fabales <br> - - - - - Fabaceae <br> - - - - - - <i>Sindora</i> <br> - - - - - - <i>Cynometra</i> <br> - - - - - - - <i>Cynometra mirabilis</i> <br> - - - - - - <i>Fordia</i> <br> - - - - - - - <i>Fordia brachybotrys</i> <br> - - - - - - - <i>Fordia splendidissima</i> <br> - - - - - - <i>Dialium</i> <br> - - - - - - - <i>Dialium indum</i> <br> - - - - - - - <i>Dialium kunstleri</i> <br> - - - - - - <i>Crudia</i> <br> - - - - - - - <i>Crudia reticulata</i> <br> - - - - - - - <i>Crudia tenuipes</i> <br> - - - - - - <i>Spatholobus</i> <br> - - - - - - - <i>Spatholobus macropterus</i> <br> - - - - - - <i>Archidendron</i> <br> - - - - - - - <i>Archidendron clypearia</i> <br> - - - - - Polygalaceae <br> - - - - - - <i>Xanthophyllum</i> <br> - - - - - - - <i>Xanthophyllum flavescens</i> <br> - - - - Magnoliales <br> - - - - - Myristicaceae <br> - - - - - - <i>Knema</i> <br> - - - - - - - <i>Knema glauca</i> <br> - - - - - - - <i>Knema latifolia</i> <br> - - - - - - - <i>Knema laurina</i> <br> - - - - - - - <i>Knema oblongata</i> <br> - - - - - - <i>Horsfieldia</i> <br> - - - - - - - <i>Horsfieldia crassifolia</i> <br> - - - - - - <i>Myristica</i> <br> - - - - - - - <i>Myristica smythiesii</i> <br> - - - - - Annonaceae <br> - - - - - - <i>Cyathocalyx</i> <br> - - - - - - <i>Monoon</i> <br> - - - - - - <i>Stelechocarpus</i> <br> - - - - - - - <i>Stelechocarpus cauliflorus</i> <br> - - - - - - <i>Phaeanthus</i> <br> - - - - - - - <i>Phaeanthus splendens</i> <br> - - - - - - <i>Pseuduvaria</i> <br> - - - - - - - <i>Pseuduvaria borneensis</i> <br> - - - - - - <i>Xylopia</i> <br> - - - - - - - <i>Xylopia ferruginea</i> <br> - - - - - - - <i>Xylopia stenopetala</i> <br> - - - - - - <i>Neo-uvaria</i> <br> - - - - - - - <i>Neo-uvaria acuminatissima</i> <br> - - - - - - <i>Miliusa</i> <br> - - - - - - - <i>Miliusa macropoda</i> <br> - - - - - - <i>Orophea</i> <br> - - - - - - - <i>Orophea myriantha</i> <br> - - - - - - <i>Polyalthia</i> <br> - - - - - - - <i>Polyalthia obliqua</i> <br> - - - - - - <i>Sageraea</i> <br> - - - - - - - <i>Sageraea elliptica</i> <br> - - - - - - <i>Maasia</i> <br> - - - - - - - <i>Maasia sumatrana</i> <br> - - - - - Magnoliaceae <br> - - - - - - <i>Magnolia</i> <br> - - - - - - - <i>Magnolia borneensis</i> <br> - - - - - - - <i>Magnolia liliifera</i> <br> - - - - - - - <i>Magnolia tsiampacca</i> <br> - - - - Asterales <br> - - - - - Asteraceae <br> - - - - - - <i>Mikania</i> <br> - - - - - - - <i>Mikania micrantha</i> <br> - - - - Laurales <br> - - - - - Lauraceae <br> - - - - - - <i>Actinodaphne</i> <br> - - - - - - <i>Beilschmiedia</i> <br> - - - - - - - <i>Beilschmiedia micrantha</i> <br> - - - - - - <i>Beilschmiedia</i> <br> - - - - - - - <i>Beilschmiedia micrantha</i> <br> - - - - - - <i>Litsea</i> <br> - - - - - -