Semantic 3D Reconstruction with Finite Element Bases

We propose a novel framework for the discretisation of multi-label problems on arbitrary, continuous domains. Our work bridges the gap between general FEM discretisations, and labeling problems that arise in a variety of computer vision tasks, including for instance those derived from the generalised Potts model. Starting from the popular formulation of labeling as a convex relaxation by functional lifting, we show that FEM discretisation is valid for the most general case, where the regulariser is anisotropic and non-metric. While our findings are generic and applicable to different vision problems, we demonstrate their practical implementation in the context of semantic 3D reconstruction, where such regularisers have proved particularly beneficial. The proposed FEM approach leads to a smaller memory footprint as well as faster computation, and it constitutes a very simple way to enable variable, adaptive resolution within the same model

Unwind: Interactive Fish Straightening

The ScanAllFish project is a large-scale effort to scan all the world's 33,100 known species of fishes. It has already generated thousands of volumetric CT scans of fish species which are available on open access platforms such as the Open Science Framework. To achieve a scanning rate required for a project of this magnitude, many specimens are grouped together into a single tube and scanned all at once. The resulting data contain many fish which are often bent and twisted to fit into the scanner. Our system, Unwind, is a novel interactive visualization and processing tool which extracts, unbends, and untwists volumetric images of fish with minimal user interaction. Our approach enables scientists to interactively unwarp these volumes to remove the undesired torque and bending using a piecewise-linear skeleton extracted by averaging isosurfaces of a harmonic function connecting the head and tail of each fish. The result is a volumetric dataset of a individual, straight fish in a canonical pose defined by the marine biologist expert user. We have developed Unwind in collaboration with a team of marine biologists: Our system has been deployed in their labs, and is presently being used for dataset construction, biomechanical analysis, and the generation of figures for scientific publication

3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations

BSP-fields: An Exact Representation of Polygonal Objects by Differentiable Scalar Fields Based on Binary Space Partitioning

The problem considered in this work is to find a dimension independent algorithm for the generation of signed scalar fields exactly representing polygonal objects and satisfying the following requirements: the defining real function takes zero value exactly at the polygonal object boundary; no extra zero-value isosurfaces should be generated; C1 continuity of the function in the entire domain. The proposed algorithms are based on the binary space partitioning (BSP) of the object by the planes passing through the polygonal faces and are independent of the object genus, the number of disjoint components, and holes in the initial polygonal mesh. Several extensions to the basic algorithm are proposed to satisfy the selected optimization criteria. The generated BSP-fields allow for applying techniques of the function-based modeling to already existing legacy objects from CAD and computer animation areas, which is illustrated by several examples