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Simulation Model for Three-Channel Luminescent Images of Cancer Cell Populations

JOURNAL OF APPLIED SPECTROSCOPY 2015年第6期81卷 996-1003页

作者： Lisitsa, E. V. Yatskou, M. M. Apanasovich, V. V. Apanasovich, T. V. Shytsik, M. M. Belorussian State Univ Minsk 220030 BELARUS

We have developed a simulation model for three-channel luminescent images of cancer cells. We do a comparative analysis of two methods for segmentation of objects within three-channel luminescent images, employed in the CellProfiler and CellDataMiner software packages, using simulated and experimental data as examples. We have studied the functional efficiency of the segmentation algorithms under high photoelectron multiplier noise conditions. Our simulation model allows us to simplify selection of the algorithm for analysis of the data during biophysical studies, with the aim of automating procedures for processing luminescent images.

关键词： luminescence microscopy cell simulation model segmentation algorithm

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Ceramics and defects Infrared thermography and numerical simulations-a wide-ranging view for quantitative analysis

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JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY 2016年第1期123卷 43-62页

作者： Sfarra, Stefano Perilli, Stefano Paoletti, Domenica Ambrosini, Dario Univ Aquila Las ER Lab Dept Ind & Informat Engn & Econ DIIIE I-67100 Laquila AQ Italy

The feasibility of square-pulsed thermography nondestructive testing for the detection of defects in one ceramic material sample has been carried out by finite element (FE) analysis. In particular, a ceramic plate containing defects of different diameters, depths, locations, nature, and shapes has been numerically investigated by means of Comsol(A (R)) Multiphysics computer program, taking into account the results coming from both a MATLAB (TM) script and the infrared thermography (IRT) technique. Indeed, the FE method simulates through a 3D model the heat transfer process induced into the ceramic material by two halogen lamps that have been applied in order to provoke an optimum thermal stress. Moreover, further defects like cracks arose beneath the surface of the plate due to the shrinkage process, have been discovered, and contrasted using a non-usual segmentation algorithm that when correlated in the time to IRT data simulates the thermo-elastic effect. Following the non-direct procedure proposed, both the depth of each defect and its main dimensions have been retrieved into a satisfactory accuracy.

关键词： Nondestructive testing Defects Inclusions Modeling Thermal properties of the pottery Silica Infrared thermography segmentation algorithm

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A Parallelizable Framework for Segmenting Piecewise Signals

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IEEE ACCESS 2019年 7卷 13217-13229页

作者： Duan, Junbo Soussen, Charles Brie, David Idier, Jerome Wang, Yu-Ping Wan, Mingxi Xi An Jiao Tong Univ Dept Biomed Engn Xian Shaanxi Peoples R China Univ Paris Sud Cent Supelec CNRS Univ Paris Saclay Lab Signaux & Syst F-91192 Gif Sur Yvette France Univ Lorraine CNRS Ctr Rech Automat Nancy Lorraine France Ecole Cent Nantes Lab Sci Numer Nantes Nantes France Tulane Univ Dept Biomed Engn New Orleans LA 70118 USA

Piecewise signals appear in many application fields. Here, we propose a framework for segmenting such signals based on the modeling of each piece using a parametric probability distribution. The proposed framework first models the segmentation as an optimization problem with sparsity regularization. Then, an algorithm based on dynamic programming is utilized for finding the optimal solution. However, dynamic programming often suffers from a heavy computational burden. Therefore, we further show that the proposed framework is parallelizable and propose using GPU-based parallel computing to accelerate the computation. This approach is highly desirable for the analysis of large volumes of data that are ubiquitous. The experiments on both the simulated and real genomic datasets from the next-generation sequencing demonstrate an improved performance in terms of both segmentation quality and computational speed.

关键词： Parallel computing piecewise distribution segmentation algorithm dynamic programming next generation sequencing

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RECOGNITION OF UNDERWATER TRANSIENT PATTERNS

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PATTERN RECOGNITION 1985年第6期18卷 485-490页

作者： CHEN, CH Electrical and Computer Engineering Department Southeastern Massachusetts University North Dartmouth MA 02747 U.S.A

Underwater transients present an unusual but unique recognition problem in that pattern characteristics and categories are not well defined, and the patterns are highly nonstationary. This paper examines the characterization, segmentation and classification of the transient events. A comparison with speech processing and recognition is also made. Although it is difficult to fully characterize the transient data, it is shown that by extracting event portions of the transient waveform through segmentation, a low order autoregressive model can provide an effective feature set for cluster analysis and event classification. Both the segmentation procedure and the recognition experiments with real data are presented in detail.

关键词： Underwater transients segmentation algorithm Autoregressive model Feature extraction Cluster analysis Event classification

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Quantification of double-layer Ni/YSZ fuel cell anodes from focused ion beam tomography data

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JOURNAL OF POWER SOURCES 2014年 246卷 819-830页

作者： Joos, Jochen Ender, Moses Rotscholl, Ingo Menzler, Norbert H. Ivers-Tiffee, Ellen Karlsruhe Inst Technol IWE D-76131 Karlsruhe Germany Forschungszentrum Julich GmbH Inst Energy & Climate Res IEK 1 D-52425 Julich Germany

Three-dimensional microstructure reconstructions of Ni yttria-stabilized zirconia (Ni/YSZ) anodes are presented, all of which are based on focused ion beam tomography data. The reconstruction procedure, starting from a series of 2D scanning electron micrographs, is investigated step by step and potential sources of error are identified. The distinction between Ni phase, YSZ phase and pore phase is solved by an advanced algorithm, which belongs to the region-growing image segmentation methods. This improves the accuracy of automated grayscale segmentation especially for images with low contrast, which is characteristic of both solid phases in Ni/YSZ anodes. Critical microstructure parameters like material fractions, surface areas, particle size and distribution of Ni, YSZ, and pore phase, as well as phase connectivity and triple-phase boundary density, are evaluated and discussed. In this contribution, two types of high-performance Ni/YSZ anodes differing in thickness of both the anode functional layer and the anode substrate are reconstructed and compared to each other. For the first time, the anode functional layer adjacent to the thin film electrolyte is separately quantified. The presented methods are qualified to quantitatively compare different anode microstructures and relate the result to their electrochemical performance. (C) 2013 Elsevier B.V. All rights reserved.

关键词： SOFC Ni/YSZ anode Focused ion beam (FIB) Microstructure reconstruction segmentation algorithm Voxel

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Online path planning of pork cutting robot using 3D laser point cloud

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INDUSTRIAL ROBOT-THE INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH AND APPLICATION 2024年第3期51卷 511-517页

作者： Liu, Yi Ning, Rui Du, Mingxin Yu, Shuanghe Yan, Yan Dalian Maritime Univ Coll Marine Elect Engn Dalian Peoples R China

Purpose - The purpose of this paper is to propose an new online path planning method for porcine belly cutting. With the proliferation in demand for the automatic systems of pork production, the development of efficient and robust meat cutting algorithms are hot issues. The uncertain and dynamic nature of the online porcine belly cutting imposes a challenge for the robot to identify and cut efficiently and accurately. Based on the above challenges, an online porcine belly cutting method using 3D laser point cloud is proposed. Design/methodology/approach - The robotic cutting system is composed of an industrial robotic manipulator, customized tools, a laser sensor and a PC. Findings - Analysis of experimental results shows that by comparing with machine vision, laser sensor-based robot cutting has more advantages, and it can handle different carcass sizes. Originality/value - An image pyramid method is used for dimensionality reduction of the 3D laser point cloud. From a detailed analysis of the outward and inward cutting errors, the outward cutting error is the limiting condition for reducing the segments by segmentation algorithm.

关键词： Online cutting path planning Porcine belly cutting 3D laser point cloud Covariance matrix segmentation algorithm

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Multilevel framework to handle object occlusions for real-time tracking

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IET IMAGE PROCESSING 2016年第11期10卷 885-892页

作者： Cai, Yingfeng Wang, Hai Chen, Xiaobo Chen, Long Jiangsu Univ Automot Engn Res Inst Zhenjiang 212013 Peoples R China Jiangsu Univ Sch Automot & Traff Engn Zhenjiang 212013 Peoples R China

This study proposes an efficient method to handle the object occlusions seen in monocular traffic image sequences. The motivation of this study is different methods perform differently in occlusion segmentation and the authors' idea is to use a situation-driven approach to aggregate different methods in order to get a good performance. This study classifies occlusion into four categories according to the foreground situation and a multilevel occlusion handling framework is utilised. First, the image segmentation algorithm based on convex hull analysis is utilised for intra-frame level occlusion segmentation. The segmentation algorithm is established by the compactness ratio and interior distance ratio of the foreground. Second, an online sample-based classification algorithm is utilised for tracking level occlusion segmentation. Training samples are extracted from the historical frames before occlusion and testing samples are extracted from the current frame by an adaptive searching strategy. The segmentation of occlusion is transferred into the online classification of testing samples. Such algorithm is established by the similarity and coherence of target's property between continuous frames. Experiments on video sequences illustrate the good performance of the proposed method under different conditions with low computational cost.

关键词： image sequences image segmentation feature extraction object occlusions real-time tracking monocular traffic image sequences multilevel occlusion handling image segmentation convex hull analysis intra-frame level occlusion segmentation segmentation algorithm online sample-based classification algorithm video sequences

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Expediting adenovirus titer assays via an algorithmic live-cell imaging technique

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JOURNAL OF BIOTECHNOLOGY 2024年 395卷 216-227页

作者： Velikonja, Claire Steenbakkers, Landon How, Joshua Enns, Mackenzie Corbett, Brandon Mccready, Chris Nease, Jake Mhaskar, Prashant Latulippe, David McMaster Univ Dept Chem Engn Hamilton ON Canada Sartorius Canada Inc Oakville ON Canada

Interest in virus-based therapeutics for the treatment of genetic and oncolytic diseases has created a demand for high-yield, low-cost virus-manufacturing processes. However, traditional analytical methods of assessing infectious virus titer require multiple processing steps and manual counting, limiting sample throughput, and increasing human error. This bottleneck severely limits the development of new manufacturing unit operations to drive down costs. In this work, we utilize an Incucyte Live-Cell Analysis System to develop a high-throughput infectious titer assay for adenovirus expressing a GFP-transgene. Although previous studies have demonstrated live-cell imaging's potential for use with other viruses, they provide little guidance regarding the selection of the viewing and analysis parameters. To fill this gap, we develop an algorithmic approach to identify the optimum viewing and analysis parameters and create a statistical workflow for quantifying infectious adenovirus in a sample dilution series in a standard 24-well microplate. The developed assay is comparable to Hexon staining, the gold-standard for adenovirus infectious titer, with a Pearson correlation coefficient of 0.9. Finally, the developed algorithmic approach and statistical workflow were applied to create an assay for adenovirus titer using a 96-well microplate, allowing five times more samples to be quantified compared to the standard 24-well plate. While this assay uses a GFP-insert that precludes its use in a clinical environment, the key learnings surrounding the careful use of viewing and analysis parameters, and the statistical workflow are widely applicable to implementing life-cell imaging for dilution-series-based assays. Moreover, this method directly enables the fast and accurate evaluation of virus samples in a preclinical environment.

关键词： Live-Cell Imaging System Adenovirus Infectious virus titer segmentation algorithm Biotherapeutic manufacturing

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Semiautomatic analysis of phase contrast magnetic resonance imaging of cerebrospinal fluid flow through the aqueduct of Sylvius

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MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2006年第2期19卷 78-87页

作者： Florez, Yudy Natalia Moratal, David Forner, Juana Marti-Bonmati, Luis Arana, Estanislao Guajardo-Hernandez, Ulises Millet-Roig, Jose Resonancia Magnet Serv Radiol Clin Quiron Valencia 46010 Spain Univ Politecn Valencia Grp BET E-46071 Valencia Spain Hosp Univ Dr Peset Valencia Spain

Objective: Quantification of the cerebrospinal fluid (CSF) flow through the aqueduct of Sylvius by means of magnetic resonance imaging (MRI) is subject to interobserver variability due to the region of interest (ROI) selection. Our objective is to develop a semiautomatic measurement method to achieve reproducible quantitative analysis of CSF flow rate and stroke volume. Material and methods: MR examinations were performed using a 1.5 T scanner with a phase contrast sequence (velocity. encoding [V-enc] of 20 cm/s, FOV = 160, 3 mm slice thickness, image matrix size 256 x 256, TR = 53 ms, TE = I I ms, NSA = 2, flip angle = 15 degrees and 23 frames per cardiac cycle with peripheral retrospective pulse gating). Our method was developed using MATLAB R7. Errors introduced by background offset and possible aliased pixels were automatically detected and corrected if necessary in order to calculate the flow parameters that characterize CSF dynamics. The semiautomatic seed method reproducibility was evaluated and compared with the radius method by two observers analysing 21 healthy subjects. Results: The measurements using the semiautomatic seed method reduced the interobservers variability (intra-class correlation [ICC] = 1.0 for stroke volume and for volumetrie flow rate) versus the radius method (ICC = 0.46 for stroke volume and 0.65 for flow rate). Normal stroke volume (39.19 +/- 20.13 mu l/cyele), flow rate (3.81 +/- 2.81 ml/min), maximal mean systolic velocity (5.27 +/- 1.3 cm/s) and maximal mean diastolic velocity (4.20 +/- 1.4 cm/s) were calculated with the half moon and aliasing corrected seed method. Conclusions: Semiautomatic measurements (seed method with half moon background and aliasing correction) allow a generalization of the calculus of flow parameters with great consistency and independency of the operator.

关键词： aliasing correction cerebrospinal fluid magnetic resonance phase imaging segmentation algorithm

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A shifting level model algorithm that identifies aberrations in array-CGH data

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BIOSTATISTICS 2010年第2期11卷 265-280页

作者： Magi, Alberto Benelli, Matteo Marseglia, Giuseppina Nannetti, Genni Scordo, Maria Rosaria Torricelli, Francesca Univ Florence Diagnost Genet Unit Careggi Hosp AOUC I-50141 Florence Italy Univ Florence Ctr Study Complex Dynam I-50019 Florence Italy Univ Florence Dept Med & Surg Crit Care Florence Italy Univ Florence Infantile Neuropsychiat Unit Careggi Hosp AOUC I-50141 Florence Italy

Array comparative genomic hybridization (aCGH) is a microarray technology that allows one to detect and map genomic alterations. The goal of aCGH analysis is to identify the boundaries of the regions where the number of DNA copies changes (breakpoint identification) and then to label each region as loss, neutral, or gain (calling). In this paper, we introduce a new algorithm, based on the shifting level model (SLM), with the aim of locating regions with different means of the log(2) ratio in genomic profiles obtained from aCGH data. We combine the SLM algorithm with the CGHcall calling procedure and compare their performances with 5 state-of-the-art methods. When dealing with synthetic data, our method outperforms the other 5 algorithms in detecting the change in the number of DNA copies in the most challenging situations. For real aCGH data, SLM is able to locate all the cytogenetically mapped aberrations giving a smaller number of false-positive breakpoints than the compared methods. The application of the SLM algorithm is not limited to aCGH data. Our approach can also be used for the analysis of several emerging experimental strategies such as high-resolution tiling array.

关键词： array-CGH segmentation algorithm Shifting level model

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