scholarly journals Spatio-temporal Image Analysis for Longitudinal and Time-Series Image Data

2018 ◽  
Author(s):  
Hanqing Zhang ◽  
Niklas Söderholm ◽  
Linda Sandblad ◽  
Krister Wiklund ◽  
Magnus Andersson

AbstractMotivationQuantitative image analysis of growing filamentous fungi and prokaryotes are important to detect and evaluate morphological effects of growth conditions, compounds and mutations. However, analysis of time-series image data is often limited by the ability of the algorithms to accurately segment structures that are complicated or if an organism is within a crowded population. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data as well as single images to find multiple filamentous structures e.g., filamentous prokaryotes, yeasts and molds using a dynamic segmentation approach. DSeg automatically segments and analyzes objects, includes drift correction, and outputs statistical data such as persistence length, growth rate and growth direction.Availability and implementationDSeg is a free open-source program written in MATLAB. DSeg can be downloaded as a package from https://sourceforge.net/projects/[email protected] and [email protected] informationSupplementary data are available at online.


2016 ◽  
Vol 64 (7) ◽  
Author(s):  
Johannes Stegmaier ◽  
Benjamin Schott ◽  
Eduard Hübner ◽  
Manuel Traub ◽  
Maryam Shahid ◽  
...  

AbstractNew imaging techniques enable visualizing and analyzing a multitude of unknown phenomena in many areas of science at high spatio-temporal resolution. The rapidly growing amount of image data, however, can hardly be analyzed manually and, thus, future research has to focus on automated image analysis methods that allow one to reliably extract the desired information from large-scale multidimensional image data. Starting with infrastructural challenges, we present new software tools, validation benchmarks and processing strategies that help coping with large-scale image data. The presented methods are illustrated on typical problems observed in developmental biology that can be answered, e.g., by using time-resolved 3D microscopy images.


Author(s):  
Robert W. Mackin

This paper presents two advances towards the automated three-dimensional (3-D) analysis of thick and heavily-overlapped regions in cytological preparations such as cervical/vaginal smears. First, a high speed 3-D brightfield microscope has been developed, allowing the acquisition of image data at speeds approaching 30 optical slices per second. Second, algorithms have been developed to detect and segment nuclei in spite of the extremely high image variability and low contrast typical of such regions. The analysis of such regions is inherently a 3-D problem that cannot be solved reliably with conventional 2-D imaging and image analysis methods.High-Speed 3-D imaging of the specimen is accomplished by moving the specimen axially relative to the objective lens of a standard microscope (Zeiss) at a speed of 30 steps per second, where the stepsize is adjustable from 0.2 - 5μm. The specimen is mounted on a computer-controlled, piezoelectric microstage (Burleigh PZS-100, 68/μm displacement). At each step, an optical slice is acquired using a CCD camera (SONY XC-11/71 IP, Dalsa CA-D1-0256, and CA-D2-0512 have been used) connected to a 4-node array processor system based on the Intel i860 chip.


Author(s):  
Carlos A. Severiano ◽  
Petrônio de Cândido de Lima e Silva ◽  
Miri Weiss Cohen ◽  
Frederico Gadelha Guimarães

Drones ◽  
2020 ◽  
Vol 5 (1) ◽  
pp. 1
Author(s):  
Geonung Park ◽  
Kyunghun Park ◽  
Bonggeun Song

Water quality deterioration due to outdoor loading of livestock manure requires efficient management of outside manure piles (OMPs). This study was designed to investigate OMPs using unmanned aerial vehicles (UAVs) for efficient management of non-point source pollution in agricultural areas. A UAV was used to acquire image data, and the distribution and cover installation status of OMPs were identified through ortho-images; the volumes of OMP were calculated using digital surface model (DSM). UAV- and terrestrial laser scanning (TLS)-derived DSMs were compared for identifying the accuracy of calculated volumes. The average volume accuracy was 92.45%. From April to October, excluding July, the monthly average volumes of OMPs in the study site ranged from 64.89 m3 to 149.69 m3. Among the 28 OMPs investigated, 18 were located near streams or agricultural waterways. Establishing priority management areas among the OMP sites distributed in a basin is possible using spatial analysis, and it is expected that the application of UAV technology will contribute to the efficient management of OMPs and other non-point source pollutants.


2020 ◽  
Vol 72 (1) ◽  
Author(s):  
Masayuki Kano ◽  
Shin’ichi Miyazaki ◽  
Yoichi Ishikawa ◽  
Kazuro Hirahara

Abstract Postseismic Global Navigation Satellite System (GNSS) time series followed by megathrust earthquakes can be interpreted as a result of afterslip on the plate interface, especially in its early phase. Afterslip is a stress release process accumulated by adjacent coseismic slip and can be considered a recovery process for future events during earthquake cycles. Spatio-temporal evolution of afterslip often triggers subsequent earthquakes through stress perturbation. Therefore, it is important to quantitatively capture the spatio-temporal evolution of afterslip and related postseismic crustal deformation and to predict their future evolution with a physics-based simulation. We developed an adjoint data assimilation method, which directly assimilates GNSS time series into a physics-based model to optimize the frictional parameters that control the slip behavior on the fault. The developed method was validated with synthetic data. Through the optimization of frictional parameters, the spatial distributions of afterslip could roughly (but not in detail) be reproduced if the observation noise was included. The optimization of frictional parameters reproduced not only the postseismic displacements used for the assimilation, but also improved the prediction skill of the following time series. Then, we applied the developed method to the observed GNSS time series for the first 15 days following the 2003 Tokachi-oki earthquake. The frictional parameters in the afterslip regions were optimized to A–B ~ O(10 kPa), A ~ O(100 kPa), and L ~ O(10 mm). A large afterslip is inferred on the shallower side of the coseismic slip area. The optimized frictional parameters quantitatively predicted the postseismic GNSS time series for the following 15 days. These characteristics can also be detected if the simulation variables can be simultaneously optimized. The developed data assimilation method, which can be directly applied to GNSS time series following megathrust earthquakes, is an effective quantitative evaluation method for assessing risks of subsequent earthquakes and for monitoring the recovery process of megathrust earthquakes.


2021 ◽  
Vol 259 ◽  
pp. 112394
Author(s):  
Huijin Yang ◽  
Bin Pan ◽  
Ning Li ◽  
Wei Wang ◽  
Jian Zhang ◽  
...  

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