An open source tool named SimpleTree, capable of modelling highly accurate cylindrical tree models from terrestrial laser scan point clouds, is presented and evaluated. All important functionalities, accessible in the software via buttons and dialogues, are described including the explanation of all necessary input parameters. The method is validated utilizing 101 point clouds of six different tree species, in the main evergreen and coniferous trees. All scanned trees have been destructively harvested to get accurate estimates of above ground biomass with which we assess the accuracy of the SimpleTree-reconstructed cylinder models. The trees were grouped into four data sets and for each one a Concordance Correlation Coefficient of at least 0.92 (0.92, 0.97, 0.92, 0.94) and an total relative error at most ~8 % (2.42%, 3.59%, –4.59%, 8.27%) was achieved in the comparison of the model results to the ground truth data. A global statistical improvement of derived cylinder radii is presented as well as an efficient optimization approach to automatically improve user given input parameters. An additional check of the SimpleTree results is presented via comparison to the results of trees reconstructed using an alternative, published method.

This paper presents a method for fitting cylinders into a point cloud, derived from a terrestrial laser-scanned tree. Utilizing high scan quality data as the input, the resulting models describe the branching structure of the tree, capable of detecting branches with a diameter smaller than a centimeter. The cylinders are stored as a hierarchical tree-like data structure encapsulating parent-child neighbor relations and incorporating the tree’s direction of growth. This structure enables the efficient extraction of tree components, such as the stem or a single branch. The method was validated both by applying a comparison of the resulting cylinder models with ground truth data and by an analysis between the input point clouds and the models. Tree models were accomplished representing more than 99% of the input point cloud, with an average distance from the cylinder model to the point cloud within sub-millimeter accuracy. After validation, the method was applied to build two allometric models based on 24 tree point clouds as an example of the application. Computation terminated successfully within less than 30 min. For the model predicting the total above ground volume, the coefficient of determination was 0.965, showing the high potential of terrestrial laser-scanning for forest inventories.

This paper presents a method for predicting the above ground leafless biomass of trees in a non destructive way. We utilize terrestrial laserscan data to predict the volume of the trees. Combining volume estimates with density measurements leads to biomass predictions. Thirty-six trees of three different species are analyzed: evergreen coniferous Pinus massoniana, evergreen broadleaved Erythrophleum fordii and leafless deciduous Quercus petraea. All scans include a large number of noise points; denoising procedures are presented in detail. Density values are considered to be a minor source of error in the method if applied to stem segments, as comparison to ground truth data reveals that prediction errors for the tree volumes are in accordance with biomass prediction errors. While tree compartments with a diameter larger than 10 cm can be modeled accurately, smaller ones, especially twigs with a diameter smaller than 4 cm, are often largely overestimated. Better prediction results could be achieved by applying a biomass expansion factor to the biomass of compartments with a diameter larger than 10 cm. With this second method the average prediction error for Q. petraea could be reduced from 33.84% overestimation to 3.56%. E. fordii results could also be improved reducing the average prediction error from

The 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 coefficient CCC of 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 the Reverse Pipe Radius Branchorder ( RPRB ) as the square root of the number of supported twigs. The prediction model radius = B ₀ * RPRB relies 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 a CCC of 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 the GrowthVolume published in earlier works, but also other parameters such as the GrowthLength, VesselVolume and RPRB which we define in this manuscript. Upload statement: Self-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.