scholarly journals Quantifying barley morphology using the Euler Characteristic Transform

2021 ◽  
Author(s):  
Erik Amezquita ◽  
Michelle Quigley ◽  
Tim Ophelders ◽  
Jacob B Landis ◽  
Daniel Koenig ◽  
...  
2021 ◽  
Author(s):  
Erik J. Amézquita ◽  
Michelle Y. Quigley ◽  
Tim Ophelders ◽  
Jacob B. Landis ◽  
Daniel Koenig ◽  
...  

AbstractShape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare, and analyze this information embedded in a robust and concise way, we turn to Topological Data Analysis (TDA), specifically the Euler Characteristic Transform (ECT). TDA measures shape comprehensively using mathematical terms based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to quantify the morphology of 3121 barley seeds scanned with X-ray Computed Tomography (CT) technology at 127 micron resolution. The ECT measures shape by analyzing topological features of an object at thresholds across a number of directional axes. We optimize the number of directions and thresholds for classification to 158 and 8 respectively, creating vectors of length 1264 that are topological signatures for each barley seed. Using these vectors, we successfully train a support vector machine to classify 28 different accessions of barley based on the 3D shape of their grains. We observe that combining both traditional and topological descriptors classifies barley seeds to their correct accession better than using just traditional descriptors alone. This improvement suggests that TDA is thus a powerful complement to traditional morphometrics to describe comprehensively a multitude of shape nuances which are otherwise not picked up. Using TDA we can quantify aspects of phenotype that have remained “hidden” without its use, and the ECT opens the possibility of accurately reconstructing objects from their topological signatures.


Author(s):  
Erik J Amézquita ◽  
Michelle Y Quigley ◽  
Tim Ophelders ◽  
Jacob B Landis ◽  
Daniel Koenig ◽  
...  

Abstract Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare, and analyze this information embedded in a robust and concise way, we turn to Topological Data Analysis (TDA), specifically the Euler Characteristic Transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to quantify the morphology of 3121 barley seeds scanned with X-ray Computed Tomography (CT) technology at 127 micron resolution. The Euler Characteristic Transform measures shape by analyzing topological features of an object at thresholds across a number of directional axes. A Kruskal-Wallis analysis of the information encoded by the topological signature reveals that the Euler Characteristic Transform picks up successfully the shape of the crease and bottom of the seeds. Moreover, while traditional shape descriptors can cluster the seeds based on their accession, topological shape descriptors can cluster them further based on their panicle. We then successfully train a support vector machine (SVM) to classify 28 different accessions of barley based exclusively on the shape of their grains. We observe that combining both traditional and topological descriptors classifies barley seeds better than using just traditional descriptors alone. This improvement suggests that TDA is thus a powerful complement to traditional morphometrics to comprehensively describe a multitude of “hidden” shape nuances which are otherwise not detected.


2021 ◽  
pp. 1-26
Author(s):  
THOMAS METTLER ◽  
GABRIEL P. PATERNAIN

Abstract We associate a flow $\phi $ with a solution of the vortex equations on a closed oriented Riemannian 2-manifold $(M,g)$ of negative Euler characteristic and investigate its properties. We show that $\phi $ always admits a dominated splitting and identify special cases in which $\phi $ is Anosov. In particular, starting from holomorphic differentials of fractional degree, we produce novel examples of Anosov flows on suitable roots of the unit tangent bundle of $(M,g)$ .


2011 ◽  
Vol 148 (1) ◽  
pp. 269-294 ◽  
Author(s):  
Eric Katz ◽  
Alan Stapledon

AbstractWe construct motivic invariants of a subvariety of an algebraic torus from its tropicalization and initial degenerations. More specifically, we introduce an invariant of a compactification of such a variety called the ‘tropical motivic nearby fiber’. This invariant specializes in the schön case to the Hodge–Deligne polynomial of the limit mixed Hodge structure of a corresponding degeneration. We give purely combinatorial expressions for this Hodge–Deligne polynomial in the cases of schön hypersurfaces and matroidal tropical varieties. We also deduce a formula for the Euler characteristic of a general fiber of the degeneration.


Author(s):  
Yongqiang Liu ◽  
Laurentiu Maxim ◽  
Botong Wang

Abstract We use the non-proper Morse theory of Palais–Smale to investigate the topology of smooth closed subvarieties of complex semi-abelian varieties and that of their infinite cyclic covers. As main applications, we obtain the finite generation (except in the middle degree) of the corresponding integral Alexander modules as well as the signed Euler characteristic property and generic vanishing for rank-one local systems on such subvarieties. Furthermore, we give a more conceptual (topological) interpretation of the signed Euler characteristic property in terms of vanishing of Novikov homology. As a byproduct, we prove a generic vanishing result for the $L^2$-Betti numbers of very affine manifolds. Our methods also recast June Huh’s extension of Varchenko’s conjecture to very affine manifolds and provide a generalization of this result in the context of smooth closed sub-varieties of semi-abelian varieties.


1990 ◽  
Vol 33 (1) ◽  
pp. 79-88
Author(s):  
Sungyun Lee

The Euler characteristic of an even dimensional submanifold in a space of constant curvature is given in terms of Weyl's curvature invariants. A derivation of Chern's kinematic formula in non-Euclidean space is completed. As an application of above results Weyl's tube formula about an odd-dimensional submanifold in a space of constant curvature is obtained.


1996 ◽  
Vol 05 (04) ◽  
pp. 427-439 ◽  
Author(s):  
RICCARDO BENEDETTI ◽  
CARLO PETRONIO

In this paper we discuss the beautiful idea of Justin Roberts [7] (see also [8]) to re-obtain the Turaev-Viro invariants [11] via skein theory, and re-prove elementarily the Turaev-Walker theorem [9], [10], [13]. We do this by exploiting the presentation of 3-manifolds introduced in [1], [4]. Our presentation supports in a very natural way a formal implementation of Roberts’ idea. More specifically, what we show is how to explicitly extract from an o-graph (the object by which we represent a manifold, see below), one of the framed links in S3 which Roberts uses in the construction of his invariant, and a planar diagrammatic representation of such a link. This implies that the proofs of invariance and equality with the Turaev-Viro invariant can be carried out in a completely “algebraic” way, in terms of a planar diagrammatic calculus which does not require any interpretation of 3-dimensional figures. In particular, when proving the “term-by-term” equality of the expansion of the Roberts invariant with the state sum which gives the Turaev-Viro invariant, we simultaneously apply several times the “fusion rule” (which is formally defined, strictly speaking, only in diagrammatic terms), showing that the “braiding and twisting” which a priori may exist on tetrahedra is globally dispensable. In our point of view the success of this formal “algebraic” approach witnesses a certain efficiency of our presentation of 3-manifolds via o-graphs. In this work we will widely use recoupling theory which was very clearly exposed in [2], and therefore we will avoid recalling notations. Actually, for the purpose of stating and proving our results we will need to slightly extend the class of trivalent ribbon diagrams on which the bracket can be computed. We also address the reader to the references quoted in [2], in particular for the fundamental contributions of Lickorish to this area. In our approach it is more natural to consider invariants of compact 3-manifolds with non-empty boundary. The case of closed 3-manifolds is included by introducing a correction factor corresponding to boundary spheres, as explained in §2. Our main result is actually an extension to manifolds with boundary of the Turaev-Walker theorem: we show that the Turaev-Viro invariant of such a manifold coincides (up to a factor which depends on the Euler characteristic) with the Reshetikhin-Turaev-Witten invariant of the manifold mirrored in its boundary.


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