PloidyQuantX: A Quantitative Microscopy Imaging Tool for Ploidy Quantification at Cell and Organ Level in Arabidopsis Root

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• 作者：Xavier Sevillano (20)
  Marc Ferrer (20)
  Mary-Paz Gonz谩lez-Garc铆a (21)
  Irina Pavelescu (21)
  Ana I. Ca帽o-Delgado (21)
  
  20. Grup de Recerca en Tecnologies M猫dia ; La Salle - Universitat Ramon Llull ; Barcelona ; Spain
  21. Department of Molecular Genetics ; Centre for Research in Agricultural Genomics (CRAG) ; CSIC-IRTA-UAB-UB ; Barcelona ; Spain
  
• 关键词：quantitative microscopy ; centromere quantification ; image processing ; biomedical imaging
• 刊名：Lecture Notes in Computer Science
• 出版年：2015
• 出版时间：2015
• 年：2015
• 卷：9043
• 期：1
• 页码：210-215
• 全文大小：259 KB
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  4. McGovern, S.L., Qi, Y., Pusztai, L., Symmans, W.F., Buchholz, T.A.: Centromere Protein-A, an Essential Centromere Protein, is a Prognostic Marker for Relapse in Estrogen Receptor-Positive Breast Cancer. Breast Cancer Res.聽14(3), R72 (2012)
  5. Round, E.K., Flowers, S.K., Richards, E.J. (1997) Arabidopsis thaliana Centromere Regions: Genetic Map Positions and Repetitive DNA Structure. Genome Res. 7: pp. 1045-1053
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• 作者单位：Bioinformatics and Biomedical Engineering
• 丛书名：978-3-319-16482-3
• 刊物类别：Computer Science
• 刊物主题：Artificial Intelligence and Robotics
  Computer Communication Networks
  Software Engineering
  Data Encryption
  Database Management
  Computation by Abstract Devices
  Algorithm Analysis and Problem Complexity
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1611-3349

文摘

Mapping centromere distribution in complete organs is a key step towards establishing how this couples to organ development and cell functions. In this context, quantitative microscopy tools play a key role, as they allow a precise measurement of centromere presence at both individual cell and whole organ levels. This work introduces PloidyQuantX, an imaging tool that operates on confocal microscopy image stacks. Tested on imagery obtained from whole-mount centromere Q-FISH of the Arabidopsis thaliana primary root, PloidyQuantX incorporates interactive segmentation and image analysis modules that allow quantifying the number of centromeres present in each cell nucleus, thus creating maps of centromere distribution in cells across the whole organ. Moreover, the presented tool also allows rendering three-dimensional models of each individual root cell, which makes it possible to relate their internal topology to specific cell functions.