Cell Segmentation in 3D Confocal Images using Supervoxel Merge-Forests with CNN-based Hypothesis Selection

Automated segmentation approaches are crucial to quantitatively analyze large-scale 3D microscopy images. Particularly in deep tissue regions, automatic methods still fail to provide error-free segmentations. To improve the segmentation quality throughout imaged samples, we present a new supervoxel-based 3D segmentation approach that outperforms current methods and reduces the manual correction effort. The algorithm consists of gentle preprocessing and a conservative super-voxel generation method followed by supervoxel agglomeration based on local signal properties and a postprocessing step to fix under-segmentation errors using a Convolutional Neural Network. We validate the functionality of the algorithm on manually labeled 3D confocal images of the plant Arabidopis thaliana and compare the results to a state-of-the-art meristem segmentation algorithm.Comment: 5 pages, 3 figures, 1 tabl

New characterizations of minimum spanning trees and of saliency maps based on quasi-flat zones

We study three representations of hierarchies of partitions: dendrograms (direct representations), saliency maps, and minimum spanning trees. We provide a new bijection between saliency maps and hierarchies based on quasi-flat zones as used in image processing and characterize saliency maps and minimum spanning trees as solutions to constrained minimization problems where the constraint is quasi-flat zones preservation. In practice, these results form a toolkit for new hierarchical methods where one can choose the most convenient representation. They also invite us to process non-image data with morphological hierarchies

A graph-based mathematical morphology reader

This survey paper aims at providing a "literary" anthology of mathematical morphology on graphs. It describes in the English language many ideas stemming from a large number of different papers, hence providing a unified view of an active and diverse field of research

Average Curve of n Digital Curves

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Analyses of the Watershed Transform

International audienceIn the framework of mathematical morphology, watershed transform (WT) represents a key step in image segmentation procedure. In this paper, we present a thorough analysis of some existing watershed approaches in the discrete case: WT based on flooding, WT based on path-cost minimization, watershed based on topology preservation, WT based on local condition and WT based on minimum spanning forest. For each approach, we present detailed description of processing procedure followed by mathematical foundations and algorithm of reference. Recent publications based on some approaches are also presented and discussed. Our study concludes with a classification of different watershed transform algorithms according to solution uniqueness, topology preservation, prerequisites minima computing and linearity

Discrete region merging and watersheds

incollectionThis paper summarizes some results of the authors concerning watershed divides and their use in region merging schemes.The first aspect deals with properties of watershed divides that can be used in particular for hierarchical region merging schemes. We introduce the mosaic to retrieve the altitude of points along the divide set. A desirable property is that, when two minima are separated by a crest in the original image, they are still separated by a crest of the same altitude in the mosaic. Our main result states that this is the case if and only if the mosaic is obtained through a topological thinning.The second aspect is closely related to the thinness of watershed divides. We present fusion graphs, a class of graphs in which any region can be always merged without any problem. This class is equivalent to the one in which watershed divides are thin. Topological thinnings do not always produce thin divides, even on fusion graphs. We also present the class of perfect fusion graphs, in which any pair of neighbouring regions can be merged through their common neighborhood. An important theorem states that the divides of any ultimate topological thinning are thin on any perfect fusion graph

Tie-zone : the bridge between watershed transforms and fuzzy connectedness

Orientador: Roberto de Alencar LotufoTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Eletrica e de ComputaçãoResumo: Esta tese introduz o novo conceito de transformada de zona de empate que unifica as múltiplas soluções de uma transformada de watershed, conservando apenas as partes comuns em todas estas, tal que as partes que diferem constituem a zona de empate. A zona de empate aplicada ao watershed via transformada imagem-floresta (TZ-IFT-WT) se revela um elo inédito entre transformadas de watershed baseadas em paradigmas muito diferentes: gota d'água, inundação, caminhos ótimos e floresta de peso mínimo. Para todos esses paradigmas e os algoritmos derivados, é um desafio se ter uma solução única, fina, e que seja consistente com uma definição. Por isso, propõe-se um afinamento da zona de empate, único e consistente. Além disso, demonstra-se que a TZ-IFT-WT também é o dual de métodos de segmentação baseados em conexidade nebulosa. Assim, a ponte criada entre as abordagens morfológica e nebulosa permite aproveitar avanços de ambas. Em conseqüência disso, o conceito de núcleo de robustez para as sementes é explorado no caso do watershed.Abstract: This thesis introduces the new concept of tie-zone transform that unifies the multiple solutions of a watershed transform, by conserving only the common parts among them such that the differing parts constitute the tie zone. The tie zone applied to the watershed via image-foresting transform (TZ-IFTWT) proves to be a link between watershed transforms based on very different paradigms: drop of water, flooding, optimal paths and forest of minimum weight. For all these paradigms and the derived algorithms, it is a challenge to get a unique and thin solution which is consistent with a definition. That is why we propose a unique and consistent thinning of the tie zone. In addition, we demonstrate that the TZ-IFT-WT is also the dual of segmentation methods based on fuzzy connectedness. Thus, the bridge between the morphological and the fuzzy approaches allows to take benefit from the advance of both. As a consequence, the concept of cores of robustness for the seeds is exploited in the case of watersheds.DoutoradoEngenharia de ComputaçãoDoutor em Engenharia Elétric

Aplicación del análisis de imágenes a la determinación de la orientación de fibra larga de vidrio en diferentes condiciones de proceso

El uso de materiales reforzados con fibra larga de vidrio ha evolucionado de manera creciente en los últimos años. Este hecho ha provocado que se necesite conocer el comportamiento de determinadas características mecánicas del mismo y que por lo tanto se busque una evaluación del comportamiento del mismo. El análisis de imágenes se muestra como una forma válida y eficaz en la determinación de la orientación de fibras. Por ello se ha diseñado una metodología basada en una metodología optimizada de algoritmos se consigue identificar, aislar y medir la orientación de las fibras de refuerzo en materiales compuestos. Acompañado de una técnica simple de preparación de muestras, podemos establecer un sistema de análisis efectivo. Esta metodología se ha aplicado en diversos procesos de transformación en los que habitualmente están implicados los refuerzos de fibra de vidrio en composites. Fundamentalmente se analiza el proceso de inyección, aunque no se olvidan procesos de compresión y rtm. Posteriormente se realiza el análisis del error en el que se incurre en la implementación del sistema.Ferrándiz Bou, S. (2007). Aplicación del análisis de imágenes a la determinación de la orientación de fibra larga de vidrio en diferentes condiciones de proceso [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/1855Palanci

Algorithms for the topological watershed

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