Journal Article

FZJ-2017-06824

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Fast High Resolution Volume Carving for 3D Plant Shoot Reconstruction

Scharr, H. (Corresponding author)FZJ* ; Briese, C. ; Embgenbroich, P. ; Fischbach, A.FZJ* ; Fiorani, F.FZJ* ; Müller-Linow, M.FZJ*

2017
Frontiers Media88991 Lausanne

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Please use a persistent id in citations: http://hdl.handle.net/2128/15578  doi:10.3389/fpls.2017.01680

Abstract: Volume carving is a well established method for visual hull reconstruction and has been successfully applied in plant phenotyping, especially for 3d reconstruction of small plants and seeds. When imaging larger plants at still relatively high spatial resolution (≤1 mm), well known implementations become slow or have prohibitively large memory needs. Here we present and evaluate a computationally efficient algorithm for volume carving, allowing e.g., 3D reconstruction of plant shoots. It combines a well-known multi-grid representation called “Octree” with an efficient image region integration scheme called “Integral image.” Speedup with respect to less efficient octree implementations is about 2 orders of magnitude, due to the introduced refinement strategy “Mark and refine.” Speedup is about a factor 1.6 compared to a highly optimized GPU implementation using equidistant voxel grids, even without using any parallelization. We demonstrate the application of this method for trait derivation of banana and maize plants.

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Contributing Institute(s):

1. Pflanzenwissenschaften (IBG-2)

Research Program(s):

1. 583 - Innovative Synergisms (POF3-583) (POF3-583)
2. DPPN - Deutsches Pflanzen Phänotypisierungsnetzwerk (BMBF-031A053A) (BMBF-031A053A)

Appears in the scientific report 2017

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Database coverage:
; ; ; NCBI Molecular Biology Database

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