scholarly journals De novo homology assessment from landmark data: A workflow to identify and track segmented structures in plant time series images

2021 ◽  
Author(s):  
John G. Hodge ◽  
Qing Li ◽  
Andrew N. Doust
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
De Novo ◽  
Control Function ◽  
Basic Research ◽  
Series Data ◽  
Differential Growth ◽  
Landmark Data ◽  
Clustering Approach ◽  
Time Series Images

AbstractAssessing the phenotypes underlying plant growth and development is integral to exploring the development, genetics, and evolution of morphology and plays an essential role in agronomic and basic research studies. Although various automated or semi-automated phenomic approaches have recently been developed, tools assessing differential growth of plant organs remains a key topic of interest, but one which is often difficult to analyze due to the requirements of segmenting and annotating specific structures or positions in the plant body in time-series data. To address this gap, we have developed a generalized workflow linking our previously published function, acute, with a companion function, homology, in the PlantCV environment. The homology function uses a generalized strategy of dimensionality reduction via starscape followed by hierarchical clustering through constella to identify ‘constellations’ of segments in eigenspace that represent the same landmark in consecutive images of a time-series. We devised a quality control function, constellaQC, that can test the accuracy of the clustering approach, and we use it to show that the approach accurately clustered the pseudo-landmarks derived from acute, although with several sources of error. We discuss the reasons for and consequences of these errors in automated workflows, and suggest how to develop these functions so that they can easily be repurposed for other phenomics datasets that may vary in dimensional complexity.

scholarly journals rhizoTrak: A flexible open source Fiji plugin for user-friendly manual annotation of time-series images from minirhizotrons

2019 ◽  
Author(s):  
Birgit Möller ◽  
Hongmei Chen ◽  
Tino Schmidt ◽  
Axel Zieschank ◽  
Roman Patzak ◽  
...  
Keyword(s):  
Time Series ◽  
Open Source ◽  
Data Exchange ◽  
Time Series Data ◽  
Full Range ◽  
Open Data ◽  
Series Data ◽  
Root Turnover ◽  
User Friendly ◽  
Time Series Images

AbstractBackground and aimsMinirhizotrons are commonly used to study root turnover which is essential for understanding ecosystem carbon and nutrient cycling. Yet, extracting data from minirhizotron images requires intensive annotation effort. Existing annotation tools often lack flexibility and provide only a subset of the required functionality. To facilitate efficient root annotation in minirhizotrons, we present the user-friendly open source tool rhizoTrak.Methods and resultsrhizoTrak builds on TrakEM2 and is publically available as Fiji plugin. It uses treelines to represent branching structures in roots and assigns customizable status labels per root segment. rhizoTrak offers configuration options for visualization and various functions for root annotation mostly accessible via keyboard shortcuts. rhizoTrak allows time-series data import and particularly supports easy handling and annotation of time series images. This is facilitated via explicit temporal links (connectors) between roots which are automatically generated when copying annotations from one image to the next. rhizoTrak includes automatic consistency checks and guided procedures for resolving conflicts. It facilitates easy data exchange with other software by supporting open data formats.ConclusionsrhizoTrak covers the full range of functions required for user-friendly and efficient annotation of time-series images. Its flexibility and open source nature will foster efficient data acquisition procedures in root studies using minirhizotrons.

scholarly journals A Hybrid Approach for Clustering Uncertain Time Series

2021 ◽  
Vol 28 (4) ◽  
pp. 255-267
Author(s):  
Ruizhe Ma ◽  
Xiaoping Zhu ◽  
Li Yan
Keyword(s):  
Time Series ◽  
Clustering Algorithm ◽  
Time Series Data ◽  
Knowledge Engineering ◽  
Uncertain Data ◽  
Hybrid Approach ◽  
Series Data ◽  
Adjusted Rand Index ◽  
Clustering Approach ◽  
Uncertain Time

Information uncertainty extensively exists in the real-world applications, and uncertain data process and analysis have been a crucial issue in the area of data and knowledge engineering. In this paper, we concentrate on uncertain time series data clustering, in which the uncertain values at time points are represented by probability density function. We propose a hybrid clustering approach for uncertain time series. Our clustering approach first partitions the uncertain time series data into a set of micro-clusters and then merges the micro-clusters following the idea of hierarchical clustering. We evaluate our approach with experiments. The experimental results show that, compared with the traditional UK-means clustering algorithm, the Adjusted Rand Index (ARI) of our clustering results have an obviously higher accuracy. In addition, the time efficiency of our clustering approach is significantly improved.

Graphical Exploratory Data Analysis for Categorical Longitudinal and Time Series Data

2013 ◽  
Author(s):  
Stephen J. Tueller ◽  
Richard A. Van Dorn ◽  
Georgiy Bobashev ◽  
Barry Eggleston
Keyword(s):  
Time Series ◽  
Data Analysis ◽  
Exploratory Data Analysis ◽  
Time Series Data ◽  
Series Data ◽  
Exploratory Data

Faktor-Faktor Yang Mempengaruhi Nilai Tukar Dollar Amerika Serikat Terhadap Rupiah Tahun 2000–2013

2017 ◽  
Vol 1 (2) ◽  
pp. 177-191
Author(s):  
Rizki Rahma Kusumadewi ◽  
Wahyu Widayat
Keyword(s):  
Time Series ◽  
Exchange Rate ◽  
Money Supply ◽  
Time Series Data ◽  
The United States ◽  
Economic Conditions ◽  
Series Data ◽  
Arch Model ◽  
United States Dollar ◽  
The Exchange Rate

Exchange rate is one tool to measure a country’s economic conditions. The growth of a stable currency value indicates that the country has a relatively good economic conditions or stable. This study has the purpose to analyze the factors that affect the exchange rate of the Indonesian Rupiah against the United States Dollar in the period of 2000-2013. The data used in this study is a secondary data which are time series data, made up of exports, imports, inflation, the BI rate, Gross Domestic Product (GDP), and the money supply (M1) in the quarter base, from first quarter on 2000 to fourth quarter on 2013. Regression model time series data used the ARCH-GARCH with ARCH model selection indicates that the variables that significantly influence the exchange rate are exports, inflation, the central bank rate and the money supply (M1). Whereas import and GDP did not give any influence.

An Anomaly Detection Method with Exemplar Subsequence for Time Series Data

2016 ◽  
Vol 136 (3) ◽  
pp. 363-372
Author(s):  
Takaaki Nakamura ◽  
Makoto Imamura ◽  
Masashi Tatedoko ◽  
Norio Hirai
Keyword(s):  
Time Series ◽  
Anomaly Detection ◽  
Time Series Data ◽  
Detection Method ◽  
Series Data

The Comparison of Land Subsidence between East and West Side of Bangkok, Thailand

2020 ◽  
Vol 17 (3) ◽  
pp. 1
Author(s):  
Angkana Pumpuang ◽  
Anuphao Aobpaet
Keyword(s):  
Time Series ◽  
Land Subsidence ◽  
Time Series Data ◽  
Series Data ◽  
Industrial Estates ◽  
Vertical Displacements ◽  
Land Deformation ◽  
Extensive Farming ◽  
Chao Phraya River ◽  
Set Up

The land deformation in line of sight (LOS) direction can be measured using time series InSAR. InSAR can successfully measure land subsidence based on LOS in many big cities, including the eastern and western regions of Bangkok which is separated by Chao Phraya River. There are differences in prosperity between both sides due to human activities, land use, and land cover. This study focuses on the land subsidence difference between the western and eastern regions of Bangkok and the most possible cause affecting the land subsidence rates. The Radarsat-2 single look complex (SLC) was used to set up the time series data for long term monitoring. To generate interferograms, StaMPS for Time Series InSAR processing was applied by using the PSI algorithm in DORIS software. It was found that the subsidence was more to the eastern regions of Bangkok where the vertical displacements were +0.461 millimetres and -0.919 millimetres on the western and the eastern side respectively. The districts of Nong Chok, Lat Krabang, and Khlong Samwa have the most extensive farming area in eastern Bangkok. Besides, there were also three major industrial estates located in eastern Bangkok like Lat Krabang, Anya Thani and Bang Chan Industrial Estate. By the assumption of water demand, there were forty-eight wells and three wells found in the eastern and western part respectively. The number of groundwater wells shows that eastern Bangkok has the demand for water over the west, and the pumping of groundwater is a significant factor that causes land subsidence in the area.Keywords: Subsidence, InSAR, Radarsat-2, Bangkok

Producers' Response to Changes in Prices and Marketing Policies: A Case Study of Sugarcane and Paddy in Eastern U.P. by S. C. Gupta and A. Majid. New York: Asia Publishing House, 1965.

1968 ◽  
Vol 8 (2) ◽  
pp. 308-309
Author(s):  
Mohammad Irshad Khan
Keyword(s):  
New York ◽  
Time Series ◽  
Time Series Data ◽  
Publishing House ◽  
Economic Incentives ◽  
The Other ◽  
Series Data ◽  
Poor Countries ◽  
Northern India

It is alleged that the agricultural output in poor countries responds very little to movements in prices and costs because of subsistence-oriented produc¬tion and self-produced inputs. The work of Gupta and Majid is concerned with the empirical verification of the responsiveness of farmers to prices and marketing policies in a backward region. The authors' analysis of the respon¬siveness of farmers to economic incentives is based on two sets of data (concern¬ing sugarcane, cash crop, and paddy, subsistence crop) collected from the district of Deoria in Eastern U.P. (Utter Pradesh) a chronically foodgrain deficit region in northern India. In one set, they have aggregate time-series data at district level and, in the other, they have obtained data from a survey of five villages selected from 170 villages around Padrauna town in Deoria.

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