TLS2trees: A scalable tree segmentation pipeline for TLS data

Phil Wilkes*, Mathias Disney, John Armston, Harm Bartholomeus, Lisa Bentley, Benjamin Brede, Andrew Burt, Kim Calders, Cecilia Chavana-Bryant, Daniel Clewley, Laura Duncanson, Brieanne Forbes, Sean Krisanski, Yadvinder Malhi, David Moffat, Niall Origo, Alexander Shenkin, Wanxin Yang

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)


Above-ground biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically 1 ha) using inventory measurements and allometry. In recent years, terrestrial laser scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB; however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of individual trees from plot level point clouds that are required to estimate woody volume, this is often done manually (e.g. with interactive point cloud editing software) and can be very time consuming. Here we present TLS2trees, an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2trees consists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated on 7.5 ha of TLS data captured across 10 plots of seven forest types; from open savanna to dense tropical rainforest. A total of 10,557 trees are segmented with TLS2trees: these are compared to 1281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is ±0.4 m3 and %RMSE is 60%. Segmentation performance decreases for smaller trees, for example where DBH ≤10 cm; a number of reasons are suggested including performance of semantic segmentation step. The volume and scale of TLS data captured in forest plots is increasing. It is suggested that to fully utilise this data for activities such as monitoring, reporting and verification or as reference data for satellite missions an automated processing pipeline, such as TLS2trees, is required. To facilitate improvements to TLS2trees, as well as modification for other laser scanning modes (e.g. mobile and UAV laser scanning), TLS2trees is a free and open-source software.

Original languageEnglish
Pages (from-to)3083-3099
JournalMethods in Ecology and Evolution
Issue number12
Early online date21 Oct 2023
Publication statusPublished - Dec 2023


  • above-ground biomass
  • Forest
  • FOSS
  • segmentation
  • terrestrial laser scanning


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