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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_raycloudtools commit 65c033b48e3f360fee95529856ade2125f5d579d
author bgruening
date Mon, 02 Feb 2026 17:33:59 +0000
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1 <tool id="3dtrees_raycloudtools" name="3DTrees: RayCloudTools" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="BSD-3-Clause">
2 <description>Tree instance segmentation</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <container type="docker">
9 ghcr.io/3dtrees-earth/3dtrees_rct:@TOOL_VERSION@
10 </container>
11 </requirements>
12
13 <command detect_errors="exit_code"><![CDATA[
14 python3 -u /src/run.py
15 --dataset-path '$input'
16 --output-dir .
17 # other params defined in parameters.py
18 ]]>
19 </command>
20
21 <inputs>
22 <param name="input" type="data" format="laz" label="Input Dataset (.laz)"
23 help="Input file to process"/>
24 <!-- Add your specific parameters from parameters.py -->
25 </inputs>
26
27 <outputs>
28 <data name="output" format="laz" label="Output" from_work_dir="final_results.laz"/>
29 </outputs>
30
31 <tests>
32 <test expect_num_outputs="1">
33 <param name="input" value="Example_Tree_RCT.laz"/>
34 <output name="output">
35 <assert_contents>
36 <has_size value="20k" delta="10k"/> <!-- 10-30KB -->
37 </assert_contents>
38 </output>
39 </test>
40 </tests>
41
42 <help format="markdown">
43 **What it does**
44
45 This tool performs graph-based tree instance segmentation on LiDAR point clouds using the **RayExtract** algorithm (Devereux et al., 2026) implemented as part of **RayCloudTools** (Lowe &amp; Stepanas, 2021).
46 It is platform-agnostic and works across airborne (ULS), terrestrial (TLS), and mobile (MLS) laser scanning data, as long as trees are well-represented by points along the entire tree length.
47
48 -----
49
50 **Processing Steps**
51
52 - Convert input point cloud to LAZ 1.2
53 - Import point cloud as ray cloud
54 - Extract terrain
55 - Extract trees
56 - Convert point color (segmentation result) to instance IDs
57 - Add instance IDs back to input point cloud
58
59 -----
60
61 **Output**
62
63 Original LAZ point cloud + instance IDs in extra dimension 'PredInstance'.
64
65 ***Tip:** We recommend using the '3DTrees: Tile and Merge' or '3DTrees: Smart Tile' tool to process large point clouds (workflow: tile → segment → merge)!*
66
67 -----
68
69 **Third-Party Components**
70
71 You agree to comply with the licence terms for these components as part of accessing the tool.
72
73 **RayCloudTools:** Copyright (c) 2020, Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230 | [CSIRO-Open Source Software License (variation of the BSD / MIT License)](https://github.com/csiro-robotics/raycloudtools);
74 **PDAL:** Copyright (c) 2025, Hobu, Inc. (howard@hobu.co) | [pdal License (BSD)](https://github.com/PDAL/PDAL?tab=License-1-ov-file#readme);
75 **NumPy:** Copyright (c) 2005-2025, NumPy Developers | [numpy License (BSD)](https://github.com/numpy/numpy?tab=License-1-ov-file#readme);
76 **LasPy:** Copyright (c) 2012, Grant Brown, grant.brown73 at gmail.com, Copyright (c) 2012, Howard Butler, hobu.inc at gmail.com, Copyright (c) 2020, Thomas Montaigu, thomas.montaigu@laposte.net | [laspy License](https://github.com/laspy/laspy?tab=License-1-ov-file#readme);
77 **Open3D:** Copyright (c) 2018-2023 www.open3d.org | [Open3D License (MIT)](https://github.com/isl-org/Open3D?tab=License-1-ov-file#readme).
78 </help>
79 <creator>
80 <person name="Hannah Greven" email="hannah.greven@hnee.de"/>
81 <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
82 </creator>
83 <citations>
84 <citation type="doi">10.1016/j.rse.2025.115162</citation>
85 <citation type="doi">10.1109/ACCESS.2021.3084954</citation>
86 <citation type="bibtex">
87 @misc{3dtrees_raycloudtools, title = {3Dtrees: RayCloudTools}, author = {3Dtrees-Project}, year = {2025}}
88 </citation>
89 </citations>
90 </tool>