eprintid: 10179836 rev_number: 7 eprint_status: archive userid: 699 dir: disk0/10/17/98/36 datestamp: 2023-10-26 13:50:39 lastmod: 2023-10-26 13:50:39 status_changed: 2023-10-26 13:50:39 type: article metadata_visibility: show sword_depositor: 699 creators_name: Wilkes, Phil creators_name: Disney, Mathias creators_name: Armston, John creators_name: Bartholomeus, Harm creators_name: Bentley, Lisa creators_name: Brede, Benjamin creators_name: Burt, Andrew creators_name: Calders, Kim creators_name: Chavana‐Bryant, Cecilia creators_name: Clewley, Daniel creators_name: Duncanson, Laura creators_name: Forbes, Brieanne creators_name: Krisanski, Sean creators_name: Malhi, Yadvinder creators_name: Moffat, David creators_name: Origo, Niall creators_name: Shenkin, Alexander creators_name: Yang, Wanxin title: TLS2trees: A scalable tree segmentation pipeline for TLS data ispublished: inpress divisions: UCL divisions: B03 divisions: C03 divisions: F26 keywords: above-ground biomass, Forest, FOSS, segmentation, terrestrial laser scanning note: Copyright © 2023 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society. This is an open access article under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits use, distribution and reproduction in any medium, provided the original work is properly cited. abstract: 1. 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. / 2. 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. / 3. 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. / 4. 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. date: 2023-10-21 date_type: published publisher: Wiley official_url: https://doi.org/10.1111/2041-210x.14233 oa_status: green full_text_type: pub language: eng primo: open primo_central: open_green verified: verified_manual elements_id: 2099964 doi: 10.1111/2041-210x.14233 lyricists_name: Disney, Mathias lyricists_name: Wilkes, Phillip lyricists_name: Yang, Wanxin lyricists_id: MIDIS56 lyricists_id: PTVWI50 lyricists_id: WYANG65 actors_name: Flynn, Bernadette actors_id: BFFLY94 actors_role: owner full_text_status: public publication: Methods in Ecology and Evolution issn: 2041-210X citation: Wilkes, Phil; Disney, Mathias; Armston, John; Bartholomeus, Harm; Bentley, Lisa; Brede, Benjamin; Burt, Andrew; ... Yang, Wanxin; + view all <#> Wilkes, Phil; Disney, Mathias; Armston, John; Bartholomeus, Harm; Bentley, Lisa; Brede, Benjamin; Burt, Andrew; Calders, Kim; Chavana‐Bryant, Cecilia; Clewley, Daniel; Duncanson, Laura; Forbes, Brieanne; Krisanski, Sean; Malhi, Yadvinder; Moffat, David; Origo, Niall; Shenkin, Alexander; Yang, Wanxin; - view fewer <#> (2023) TLS2trees: A scalable tree segmentation pipeline for TLS data. Methods in Ecology and Evolution 10.1111/2041-210x.14233 <https://doi.org/10.1111/2041-210x.14233>. (In press). Green open access document_url: https://discovery.ucl.ac.uk/id/eprint/10179836/1/TLS2trees%20%20A%20scalable%20tree%20segmentation%20pipeline%20for%20TLS%20data.pdf