Dataset: Census of individual trees of Hacienda San Jose Vichada (2023)

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Ruiz Hurtado, Andres Felipe; Perez Bolanos, Juliana; Arrechea Castillo, Darwin Alexis; Matiz Rubio, Natalia; Costa Junior, Ciniro; Arango Mejia, Jacobo; Cardoso Arango, Juan Andrés, 2024, "Dataset: Census of individual trees of Hacienda San Jose Vichada (2023)", https://doi.org/10.7910/DVN/NMX9VE, Harvard Dataverse, V1

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Description	This dataset contains information of estimated individual trees in Hacienda San José (HSJ), Vichada-Colombia extracted from remote sensing imagery processed using AI models and the TreeEyed QGIS Plugin. The dataset includes a CSV file with attributes related to tree dimensions and geolocation and a shapefile with polygons representing each tree. Methodology:The tree information for this dataset was obtained using a custom QGIS plugin (TreeEyed) and python scripting, designed to process high-resolution RGB remote sensing imagery to derive tree data. Leveraging AI pretrained models, in this case Meta's HighResCanopyHeight model was employed. The methodology involved processing RGB imagery with a resolution of 0.5 meters and dimensions of 42,686x30,630 pixels for the region of interest, a subdivision in 1260 tiles of 1024x1024 pixels to process and obtain canopy tree height rasters, merging, vectorizing tree instances, and filtering to isolate individual trees. Zonal statistics were then applied to assign estimated tree height values to each instance by extracting the maximum pixel value within the tree crown polygon boundary. This approach allowed for flexible and localized analysis, enabling the derivation of detailed tree metrics such as height, crown area and perimeter, and equivalent diameter from high-resolution RGB imagery. (2024-11)
Subject	Earth and Environmental Sciences; Agricultural Sciences
Keyword	remote sensing, artificial intelligence, Americas, Crops for Nutrition and Health
License/Data Use Agreement	Custom Dataset Terms

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	1 to 3 of 3 Files	Original Format Archival Format (.tab)
	01a. readme.md Markdown Text - 1.9 KB Published Nov 28, 2024 14 Downloads MD5: f55e09f104884207cca478e58f655a93 Readme file, providing an overview of the dataset Documentation	Preview "01a. readme.md" Access File File Access Public Download Options Markdown Text Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	02a. hsj_trees_2023.tab Tabular Data - 4.7 MB Published Nov 28, 2024 17 Downloads 10 Variables, 32662 Observations UNF:6:8nxnBMTyZOnvHopiOZgsDA== CSV file containing descriptive attributes for each tree. Data	Preview "02a. hsj_trees_2023.tab" Preview "02a. hsj_trees_2023.tab" Access File File Access Public Download Options Comma Separated Values (Original File Format) Tab-Delimited RData Download Metadata DDI Codebook v2 Data File Citation Download EndNote XML Download RIS Download BibTeX Explore Options Data Explorer v2
	03a. hsj_trees_2023.zip Shapefile as ZIP Archive - 3.6 MB Published Nov 28, 2024 13 Downloads MD5: 5d69de9419cb7986f1bc0baaead9d161 Compressed shapefile file containing the shapefile for the tree polygons Data	Access File File Access Public Download Options Shapefile as ZIP Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX

Citation Metadata

Persistent Identifier	doi:10.7910/DVN/NMX9VE
Publication Date	2024-11-28
Title	Dataset: Census of individual trees of Hacienda San Jose Vichada (2023)
Author	International Center for Tropical Agriculture - CIAThttps://orcid.org/0000-0003-1293-8736 International Center for Tropical Agriculture - CIAThttps://orcid.org/0009-0008-8076-724X International Center for Tropical Agriculture - CIAThttps://orcid.org/0000-0002-2395-2181 Matiz Rubio, NataliaInternational Center for Tropical Agriculture - CIAT International Center for Tropical Agriculture - CIAThttps://orcid.org/0000-0003-1854-2927 International Center for Tropical Agriculture - CIAThttps://orcid.org/0000-0002-4828-9398 International Center for Tropical Agriculture - CIAThttps://orcid.org/0000-0002-0252-4655
Point of Contact	Use email button above to contact. Alliance Data Management (Bioversity International and the International Center for Tropical Agriculture)
Description	This dataset contains information of estimated individual trees in Hacienda San José (HSJ), Vichada-Colombia extracted from remote sensing imagery processed using AI models and the TreeEyed QGIS Plugin. The dataset includes a CSV file with attributes related to tree dimensions and geolocation and a shapefile with polygons representing each tree. Methodology:The tree information for this dataset was obtained using a custom QGIS plugin (TreeEyed) and python scripting, designed to process high-resolution RGB remote sensing imagery to derive tree data. Leveraging AI pretrained models, in this case Meta's HighResCanopyHeight model was employed. The methodology involved processing RGB imagery with a resolution of 0.5 meters and dimensions of 42,686x30,630 pixels for the region of interest, a subdivision in 1260 tiles of 1024x1024 pixels to process and obtain canopy tree height rasters, merging, vectorizing tree instances, and filtering to isolate individual trees. Zonal statistics were then applied to assign estimated tree height values to each instance by extracting the maximum pixel value within the tree crown polygon boundary. This approach allowed for flexible and localized analysis, enabling the derivation of detailed tree metrics such as height, crown area and perimeter, and equivalent diameter from high-resolution RGB imagery. (2024-11)
Subject	Earth and Environmental Sciences; Agricultural Sciences
Keyword	remote sensing (AGROVOC) http://aims.fao.org/aos/agrovoc/c_6498 artificial intelligence (AGROVOC) http://aims.fao.org/aos/agrovoc/c_27064 Americas (Research Region) Crops for Nutrition and Health (Research Lever)
Topic Classification	data collection (AGROVOC) http://aims.fao.org/aos/agrovoc/c_2128 trees (AGROVOC) http://aims.fao.org/aos/agrovoc/c_7887 agroforestry (AGROVOC) http://aims.fao.org/aos/agrovoc/c_207 silvopastoral systems (AGROVOC) http://aims.fao.org/aos/agrovoc/c_16097
Language	English
Producer	Bioversity International and the International Center for Tropical Agriculture https://alliancebioversityciat.org/
Production Date	2023
Funding Information	USA-Bezos Earth Fund though Bioversity International USA, Inc .- Using genetic diversity to capture carbon through deep root systems in tropical soils (Research and Capacity development): A486
Distributor	Bioversity International and the International Center for Tropical Agriculture https://alliancebioversityciat.org/
Depositor	Alliance Data Management
Deposit Date	2024-11-25
Time Period	Start Date: 2023; End Date: 2023
Date of Collection	Start Date: 2023; End Date: 2023
Data Type	Geospatial Data; Interpolated Data; Quantitative Data; Geographic Data
Related Dataset	Ruiz Hurtado, Andres Felipe; Perez Bolanos, Juliana; Arrechea Castillo, Darwin Alexis; Cardoso Arango, Juan Andres, 2024, "Census of individual trees of Hacienda San Jose Vichada (2020)", https://doi.org/10.7910/DVN/5TEA8E, Harvard Dataverse, V1
Other Reference	Ruiz-Hurtado, A.F.; Cardoso Arango, J.A. (2024) TreeEyed: QGIS plugin for tree monitoring. [Software] Version 0.1.; Tolan, J., Yang, H.-I., Nosarzewski, B., Couairon, G., Vo, H.V., Brandt, J., Spore, J., Majumdar, S., Haziza, D., Vamaraju, J., Moutakanni, T., Bojanowski, P., Johns, T., White, B., Tiecke, T., Couprie, C., 2024. Very high resolution canopy height maps from RGB imagery using self-supervised vision transformer and convolutional decoder trained on aerial lidar. Remote Sensing of Environment 300, 113888. https://doi.org/10.1016/j.rse.2023.113888

Geospatial Metadata

Geographic Coverage	Colombia, Vichada
Geographic Bounding Box	-69.68245 -69.48948 6.00112 5.86238

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