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

Plateau Problem in the Watershed Transform

The watershed transform is one of best known and widely used methods for image segmentation in mathematical morphology. Since the definition, deriving from geology and nature observation is quite intuitive and straightforward to implement; many fast and powerful algorithms for watershed transform have already been presented. However, there still occur problems when one wishes to achieve a precise solution on blurred or noised image. The same range of problems is faced when a plateau occurs in the image. In this paper several methods for plateau reduction are discussed and some novel ideas proposed. All algorithms are performed on a set of both natural and synthetic images

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

3D + t Morphological Processing: Applications to Embryogenesis Image Analysis

We propose to directly process 3D + t image sequences with mathematical morphology operators, using a new classi?cation of the 3D+t structuring elements. Several methods (?ltering, tracking, segmentation) dedicated to the analysis of 3D + t datasets of zebra?sh embryogenesis are introduced and validated through a synthetic dataset. Then, we illustrate the application of these methods to the analysis of datasets of zebra?sh early development acquired with various microscopy techniques. This processing paradigm produces spatio-temporal coherent results as it bene?ts from the intrinsic redundancy of the temporal dimension, and minimizes the needs for human intervention in semi-automatic algorithms

Effective Cloud Detection and Segmentation using a Gradient-Based Algorithm for Satellite Imagery; Application to improve PERSIANN-CCS

Being able to effectively identify clouds and monitor their evolution is one important step toward more accurate quantitative precipitation estimation and forecast. In this study, a new gradient-based cloud-image segmentation technique is developed using tools from image processing techniques. This method integrates morphological image gradient magnitudes to separable cloud systems and patches boundaries. A varying scale-kernel is implemented to reduce the sensitivity of image segmentation to noise and capture objects with various finenesses of the edges in remote-sensing images. The proposed method is flexible and extendable from single- to multi-spectral imagery. Case studies were carried out to validate the algorithm by applying the proposed segmentation algorithm to synthetic radiances for channels of the Geostationary Operational Environmental Satellites (GOES-R) simulated by a high-resolution weather prediction model. The proposed method compares favorably with the existing cloud-patch-based segmentation technique implemented in the PERSIANN-CCS (Precipitation Estimation from Remotely Sensed Information using Artificial Neural Network - Cloud Classification System) rainfall retrieval algorithm. Evaluation of event-based images indicates that the proposed algorithm has potential to improve rain detection and estimation skills with an average of more than 45% gain comparing to the segmentation technique used in PERSIANN-CCS and identifying cloud regions as objects with accuracy rates up to 98%

Liver segmentation in MRI: a fully automatic method based on stochastic partitions

There are few fully automated methods for liver segmentation in magnetic resonance images (MRI) despite the benefits of this type of acquisition in comparison to other radiology techniques such as computed tomography (CT). Motivated by medical requirements, liver segmentation in MRI has been carried out. For this purpose, we present a new method for liver segmentation based on the watershed transform and stochastic partitions. The classical watershed over-segmentation is reduced using a marker-controlled algorithm. To improve accuracy of selected contours, the gradient of the original image is successfully enhanced by applying a new variant of stochastic watershed. Moreover, a final classifier is performed in order to obtain the final liver mask. Optimal parameters of the method are tuned using a training dataset and then they are applied to the rest of studies (17 datasets). The obtained results (a Jaccard coefficient of 0.91 +/- 0.02) in comparison to other methods demonstrate that the new variant of stochastic watershed is a robust tool for automatic segmentation of the liver in MRI. (C) 2014 Elsevier Ireland Ltd. All rights reserved.This work has been supported by the MITYC under the project NaRALap (ref. TSI-020100-2009-189), partially by the CDTI under the project ONCOTIC (IDI-20101153), by Ministerio de Educacion y Ciencia Spain, Project Game Teen (TIN2010-20187) projects Consolider-C (SEJ2006-14301/PSIC), "CIBER of Physiopathology of Obesity and Nutrition, an initiative of ISCIII" and Excellence Research Program PROMETEO (Generalitat Valenciana. Conselleria de Educacion, 2008-157). We would like to express our gratitude to the Hospital Clinica Benidorm, for providing the MR datasets and to the radiologist team of Inscanner for the manual segmentation of the MR images.López-Mir, F.; Naranjo Ornedo, V.; Angulo, J.; Alcañiz Raya, ML.; Luna, L. (2014). Liver segmentation in MRI: a fully automatic method based on stochastic partitions. Computer Methods and Programs in Biomedicine. 114(1):11-28. https://doi.org/10.1016/j.cmpb.2013.12.022S1128114

Morphological processing of stereoscopic image superimpositions for disparity map estimation

This paper deals with the problem of depth map computation from a pair of rectified stereo images and presents a novel solution based on the morphological processing of disparity space volumes. The reader is guided through the four steps composing the proposed method: the segmentation of stereo images, the diffusion of superimposition costs controlled by the segmentation, the resulting generation of a sparse disparity map which finally drives the estimation of the dense disparity map. An objective evaluation of the algorithm's features and qualities is provided and is accompanied by the results obtained on Middlebury's 2014 stereo database

Segmentation and tracking individual pseudomonas aeruginosa bacteria in dense populations of motile cells

The dynamics of individual bacteria underlies the manifestation of complex multicellular behaviours such as biofilm development and colony expansion. High resolution movies of expanding bacterial colonies reveal intriguing patterns of cell motions. A quantitative understanding of the observed behaviour in relation to the bacteria's own motile apparatus and to hydrodynamic forces requires that bacteria be identified and tracked over time. This represents a demanding undertaking as their size is close to the diffraction limit; they are very close to each other; and a typical image may contain over a thousand cells. Here, we describe the approach that we have developed to segment individual bacteria and track them in high resolution phase contrast microscopy movies. We report that over 99% of non-overlapping bacteria could be segmented correctly using mathematical morphology, and we present preliminary results that exploit this new capability. © 2009 IEEE

Topological Persistence for Relating Microstructure and Capillary Fluid Trapping in Sandstones

Results from a series of two‐phase fluid flow experiments in Leopard, Berea, and Bentheimer sandstones are presented. Fluid configurations are characterized using laboratory‐based and synchrotron based 3‐D X‐ray computed tomography. All flow experiments are conducted under capillary‐dominated conditions. We conduct geometry‐topology analysis via persistent homology and compare this to standard topological and watershed‐partition‐based pore‐network statistics. Metrics identified as predictors of nonwetting fluid trapping are calculated from the different analytical methods and are compared to levels of trapping measured during drainage‐imbibition cycles in the experiments. Metrics calculated from pore networks (i.e., pore body‐throat aspect ratio and coordination number) and topological analysis (Euler characteristic) do not correlate well with trapping in these samples. In contrast, a new metric derived from the persistent homology analysis, which incorporates counts of topological features as well as their length scale and spatial distribution, correlates very well (R2 = 0.97) to trapping for all systems. This correlation encompasses a wide range of porous media and initial fluid configurations, and also applies to data sets of different imaging and image processing protocols.We gratefully acknowledge funding from the member companies of the ANU/UNSW Digicore Research Consortium, as well as the Australian Research Council. Adrian Sheppard is supported by Discovery Project DP160104995, Vanessa Robins is supported by ARC Future Fellowship FT140100604, and Anna Herring is supported by ARC Discovery Early Career Fellowship DE180100082