Literature DB >> 25804539

Accuracy in Quantitative 3D Image Analysis.

George W Bassel1.   

Abstract

Quantitative 3D imaging is becoming an increasingly popular and powerful approach to investigate plant growth and development. With the increased use of 3D image analysis, standards to ensure the accuracy and reproducibility of these data are required. This commentary highlights how image acquisition and postprocessing can introduce artifacts into 3D image data and proposes steps to increase both the accuracy and reproducibility of these analyses. It is intended to aid researchers entering the field of 3D image processing of plant cells and tissues and to help general readers in understanding and evaluating such data.
© 2015 American Society of Plant Biologists. All rights reserved.

Mesh:

Year:  2015        PMID: 25804539      PMCID: PMC4558689          DOI: 10.1105/tpc.114.135061

Source DB:  PubMed          Journal:  Plant Cell        ISSN: 1040-4651            Impact factor:   11.277


  11 in total

1.  Computational analysis of live cell images of the Arabidopsis thaliana plant.

Authors:  Alexandre Cunha; Paul T Tarr; Adrienne H K Roeder; Alphan Altinok; Eric Mjolsness; Elliot M Meyerowitz
Journal:  Methods Cell Biol       Date:  2012       Impact factor: 1.441

2.  Elastic domains regulate growth and organogenesis in the plant shoot apical meristem.

Authors:  Daniel Kierzkowski; Naomi Nakayama; Anne-Lise Routier-Kierzkowska; Alain Weber; Emmanuelle Bayer; Martine Schorderet; Didier Reinhardt; Cris Kuhlemeier; Richard S Smith
Journal:  Science       Date:  2012-03-02       Impact factor: 47.728

3.  Integrated genetic and computation methods for in planta cytometry.

Authors:  Fernán Federici; Lionel Dupuy; Laurent Laplaze; Marcus Heisler; Jim Haseloff
Journal:  Nat Methods       Date:  2012-04-01       Impact factor: 28.547

4.  Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution.

Authors:  Romain Fernandez; Pradeep Das; Vincent Mirabet; Eric Moscardi; Jan Traas; Jean-Luc Verdeil; Grégoire Malandain; Christophe Godin
Journal:  Nat Methods       Date:  2010-06-13       Impact factor: 28.547

5.  Segmenting the sepal and shoot apical meristem of Arabidopsis thaliana.

Authors:  Alexandre L Cunha; Adrienne H K Roeder; Elliot M Meyerowitz
Journal:  Annu Int Conf IEEE Eng Med Biol Soc       Date:  2010

6.  High-resolution whole-mount imaging of three-dimensional tissue organization and gene expression enables the study of Phloem development and structure in Arabidopsis.

Authors:  Elisabeth Truernit; Hélène Bauby; Bertrand Dubreucq; Olivier Grandjean; John Runions; Julien Barthélémy; Jean-Christophe Palauqui
Journal:  Plant Cell       Date:  2008-06-03       Impact factor: 11.277

7.  A computational image analysis glossary for biologists.

Authors:  Adrienne H K Roeder; Alexandre Cunha; Michael C Burl; Elliot M Meyerowitz
Journal:  Development       Date:  2012-09       Impact factor: 6.868

8.  Genetic control of plant development by overriding a geometric division rule.

Authors:  Saiko Yoshida; Pierre Barbier de Reuille; Brendan Lane; George W Bassel; Przemyslaw Prusinkiewicz; Richard S Smith; Dolf Weijers
Journal:  Dev Cell       Date:  2014-03-27       Impact factor: 12.270

9.  Computational morphodynamics of plants: integrating development over space and time.

Authors:  Adrienne H K Roeder; Paul T Tarr; Cory Tobin; Xiaolan Zhang; Vijay Chickarmane; Alexandre Cunha; Elliot M Meyerowitz
Journal:  Nat Rev Mol Cell Biol       Date:  2011-03-02       Impact factor: 94.444

10.  Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set.

Authors:  Niko Geldner; Valérie Dénervaud-Tendon; Derek L Hyman; Ulrike Mayer; York-Dieter Stierhof; Joanne Chory
Journal:  Plant J       Date:  2009-02-26       Impact factor: 6.417

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  5 in total

1.  Cost-effective, personalized, 3D-printed liver model for preoperative planning before laparoscopic liver hemihepatectomy for colorectal cancer metastases.

Authors:  Jan Sylwester Witowski; Michał Pędziwiatr; Piotr Major; Andrzej Budzyński
Journal:  Int J Comput Assist Radiol Surg       Date:  2017-01-31       Impact factor: 2.924

2.  Topological analysis of multicellular complexity in the plant hypocotyl.

Authors:  Matthew Db Jackson; Hao Xu; Salva Duran-Nebreda; Petra Stamm; George W Bassel
Journal:  Elife       Date:  2017-07-06       Impact factor: 8.140

3.  Quantitative analysis of the 3D cell shape changes driving soybean germination.

Authors:  Nátali Maidl Souza; Alexander T Topham; George W Bassel
Journal:  J Exp Bot       Date:  2017-03-01       Impact factor: 6.992

4.  3D Reconstruction of Lipid Droplets in the Seed of Brassica napus.

Authors:  Yongtai Yin; Liangxing Guo; Kang Chen; Zhenyi Guo; Hongbo Chao; Baoshan Wang; Maoteng Li
Journal:  Sci Rep       Date:  2018-04-26       Impact factor: 4.379

5.  Routine Optical Clearing of 3D-Cell Cultures: Simplicity Forward.

Authors:  Elina Nürnberg; Mario Vitacolonna; Julia Klicks; Elena von Molitor; Tiziana Cesetti; Florian Keller; Roman Bruch; Torsten Ertongur-Fauth; Katja Riedel; Paul Scholz; Thorsten Lau; Richard Schneider; Julia Meier; Mathias Hafner; Rüdiger Rudolf
Journal:  Front Mol Biosci       Date:  2020-02-21
  5 in total

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