SimpleForest - a comprehensive tool for 3d reconstruction of trees from forest plot point clouds
Authors: Jan Hackenberg , Kim Calders , Demol Miro , Raumonen Pasi , Piboule Alexandre , Mathias Disney 
Published: July 2021

AbstractThe here-on presented SimpleForest is written in C++ and published under GPL v3. As input data SimpleForest utilizes forestry scenes recorded as terrestrial laser scan clouds. SimpleForest provides a fully automated pipeline to model the ground as a digital terrain model, then segment the vegetation and finally build quantitative structure models of trees (QSMs) consisting of up to thousands of topologically ordered cylinders. These QSMs allow us to calculate traditional forestry metrics such as diameter at breast height, but also volume and other structural metrics that are hard to measure in the field. Our volume evaluation on three data sets with destructive volumes show high prediction qualities with concordance correlation coefficientCCCof 0.91 (0.87), 0.94 (0.92) and 0.97 (0.93) for each data set respectively.We combine two common assumptions in plant modeling “The sum of cross sectional areas after a branch junction equals the one before the branch junction” (Pipe Model Theory) and “Twigs are self-similar” (West, Brown and Enquist model). As even sized twigs correspond to even sized cross sectional areas for twigs we define theReverse Pipe Radius Branchorder(RPRB) as the square root of the number of supported twigs. The prediction modelradius=B0*RPRBrelies only on correct topological information and can be used to detect and correct overestimated cylinders. In QSM building the necessity to handle overestimated cylinders is well known. The RPRB correction performs better with aCCCof 0.97 (0.93) than former published ones 0.80 (0.88) and 0.86 (0.85) in our validation.We encourage forest ecologists to analyze output parameters such as theGrowthVolumepublished in earlier works, but also other parameters such as theGrowthLength, VesselVolumeandRPRBwhich we define in this manuscript.Upload statementSelf-uploaded pre-print for peer-review submitted manuscript. The manuscript was submitted on 26th of July 2021 to Plos Computational Biology:I, Jan Hackenberg uploaded this manuscript because the automated journal upload was rejected for the following reason:Thank you for considering posting your manuscript “SimpleForest - a comprehensive tool for 3d reconstruction of tree from forest plot point clouds.” as a preprint. Your manuscript does not meet bioRxiv’s criteria and therefore we will not be sending it for posting as a preprint. For more information about our checks, see link.We have noted that it contains material that is potentially subject to copyright. In particular, screenshot in Figure 1. Preprints posted to bioRxiv following submission to PLOS journals are done so under the CC BY license. To avoid a potential breach of the copyright that applies to the material listed above, we are unable to make the manuscript publicly available.Fig 1.Submission system screenshot.Please note that this decision does not affect the editorial process at PLOS Computational Biology. Your manuscript is being separately assessed with regards to sending for peer review.From section Abstract on, the pdf you see is same as submitted one.