Tree segmentation and point cloud classification for tree damage assessment and top-kill assessment: Code repository

Project title: Evaluating a novel approach to detect the vertical structure of insect damage in trees using multispectral and three-dimensional data from drone imagery in the northern Rocky Mountains, USA

Abhinav Shrestha ¹, Jeffrey A. Hicke ¹, Arjan J. H. Meddens ², Jason W. Karl ³, and Amanda T. Stahl ²

¹ Department of Earth and Spatial Sciences, University of Idaho, Moscow, ID, USA 83844
² School of the Environment, Washington State University, Pullman, WA, USA, 99164
³ Department of Forest, Rangeland, and Fire Sciences, University of Idaho, Moscow, ID, USA 83844

Repository information:

• This GitHub repository contains necessary code and materials for combination of tree segmentation and point cloud classification for subsequent tree damage assessment and top-kill detection.

• The metholody uses functions from the lidR R package.

• The code available in the repository is to be applied to a subset data of the study site (also included in the repository).

• Please refer to the manuscript for details about the project.

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The repository contains the following directories:

• The scripts directory contains R and python scripts in numbered sub-directories that outline the methodology of this project.
• The docs directory contains housekeeping documents and figures used for the construction and maintainance of this repository.

Graphical abstract:

Details of the methodology are in the scripts directory

Code developed by:

Abhinav Shrestha
Principal investigator
MS, Department of Earth and Spatial Sciences
University of Idaho, Moscow, ID

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Current position and contact information:

Abhinav Shrestha
Remote Sensing and Geospatial Specialist, RedCastle Resources, Inc.
Federal Contractor for USDA Forest Service Geospatial Technology and Applications Center (GTAC)
Salt Lake City, UT

Contact information:

• [email protected]
• Academic website
• GitHub

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Acknowledgements

Note

The research for this project was conducted in the ancestral homelands of the Ksanka (Kootenai), Ql̓ispé (Pend d’Oreille), and Sélish (Salish) tribes of western Montana.

Drone data used for this MS thesis was collected for a broader project assessing tree damage funded by the NASA Commercial SmallSat Data Analysis (NASA CSDA) project (NASA CSDA, award #80NSSC21K115).

NASA CSDA team: Dr. Jeffrey Hicke (University of Idaho), Dr. Arjan Meddens (Washington State University (WSU)), Dr. Amanda Stahl (WSU), Luke Schefke (WSU), Dr. Andrew Hudak (US Forest Service (USFS)), Benjamin Bright (USFS).