Biology subjects

Hackenberg, J.

Publications and source records attributed to Hackenberg, J..

3 recordsLinked to original sources

bioRxiv2022

Improving quantitative structure models of trees inspired by pipe and metabolic scaling theory

PurposeWe invent in this manuscript new tree parameters which can be derived from a single QSM. QSMs are topological ordered cylinder models of trees which describe the branching structure up to the tips. All new invented parameters have in common, that their defining point of view looks from the direction of the tips and not from the root along the tree. MethodsWe use new allometric power functions to predict the radius from the invented parameters. Then we improve the radii of the QMSs cylinders utilizing those functions. ResultsFor validation we use QSMs produced from an open point cloud data set of tree clouds with SimpleForest software. We compare the QSM volume against the harvested reference data for 65felled trees. We also found QSM data of TreeQSM, a competitive and broadly accepted QSM modeling tool. Our RMSE was less than 40 % of the TreeQSM RMSE. For other error measures, the r2adj. and the CCC, the relative improvement looked even better with reaching only 27 % and 21 % of the TreeQSM errors respectively. In a second validation part we show a way to run numerical tests against the West Brown Enquist (WBE) model. Expected power coefficients have been published for various allometric relations and we compare them to predicted values from QSM data. The deviation from the expected values ranges here from 8 % underestimation to 32 % overestimation. ConclusionsQuality - With the invention of the QSM radius filter technique we improve tree volume prediction capabilities utilizing QSMs. Quantity - More data can be collected with QSMs than with traditional methods.

bioinformatics↗

bioRxiv2022

Gaining insight into the allometric scaling of trees by utilizing 3d reconstructed tree models - a SimpleForest study

Forestry utilizes volume predictor functions utilizing as input the diameter at breast height. Some of those functions take the power form Y = a * Xb. In fact this function is fundamental for the biology field of allometric scaling theories founded round about a century ago. The theory describes the relationships between organs/body parts and the complete body of organisms. With digital methods we can generate 3d forest point clouds non destructively in short time frames. SimpleForest is one free available tool which generates fully automated ground and tree models from high resoluted forest plots. Generated topological ordered cylinder models are called commonly QSMs. We use SimpleForest QSMs an build a function which estimates the total supported wood volume at any given point of the tree. As input we use the supported soft wood volume for those query points. Instead of measuring directly the soft wood volume we use as a proxy the number of supported twigs. We argue with the pipe model theory for the correctness of the proxy. We can use the named relationship to also filter our QSMs made of an open data set of tree clouds. The filter corrects overestimated radii. And we compare the corrected QSM volume against the harvested reference data for 66 felled trees. We also found QSM data of TreeQSM, a competitive and broadly accepted QSM modeling tool. Our RMSE was less than 40% of the tree QSM RMSE. And for other error measures, the r2adj. and the CCC, the relative improvement looked even better with 27% and 21% respectively. We consider this manuscript as highly impactful because of the magnitude of quality improvement we do. The relation between soft volume and total volume distributions seems to be really strong and tree data can easily also be used as example data for the generic field of allometric scaling.

bioinformatics↗

bioRxiv2021

SimpleForest - a comprehensive tool for 3d reconstruction of trees from forest plot point clouds

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 [Formula] 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 = B0 * 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 [Formula] 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 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 bioRxivs 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. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/454344v1_fig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@1094b17org.highwire.dtl.DTLVardef@120d7a3org.highwire.dtl.DTLVardef@12d2fbcorg.highwire.dtl.DTLVardef@1990a4d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 1.C_FLOATNO Submission system screenshot. C_FIG 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.

plant biology↗