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Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets

Author

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  • Ilya Belevich
  • Merja Joensuu
  • Darshan Kumar
  • Helena Vihinen
  • Eija Jokitalo

Abstract

Understanding the structure–function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis of large datasets are posing a bottleneck for the workflow. Here, we present a new software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data, which is freely available from a dedicated website. The open-source environment enables modification and insertion of new plug-ins to customize the program for specific needs. We provide practical examples of program features used for processing, segmentation and analysis of light and electron microscopy datasets, and detailed tutorials to enable users to rapidly and thoroughly learn how to use the program.This Community Page describes a freely available, open-source software that implements and integrates a range of manual and semi-automated segmentation tools for processing and quantifying light and electron microscopy data.

Suggested Citation

  • Ilya Belevich & Merja Joensuu & Darshan Kumar & Helena Vihinen & Eija Jokitalo, 2016. "Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets," PLOS Biology, Public Library of Science, vol. 14(1), pages 1-13, January.
    • Handle: RePEc:plo:pbio00:1002340
    DOI: 10.1371/journal.pbio.1002340
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    1. Jan Dettmer & Robertas Ursache & Ana Campilho & Shunsuke Miyashima & Ilya Belevich & Seana O’Regan & Daniel Leroy Mullendore & Shri Ram Yadav & Christa Lanz & Luca Beverina & Antonio Papagni & Korbini, 2014. "CHOLINE TRANSPORTER-LIKE1 is required for sieve plate development to mediate long-distance cell-to-cell communication," Nature Communications, Nature, vol. 5(1), pages 1-11, September.
    2. Moritz Helmstaedter & Kevin L. Briggman & Srinivas C. Turaga & Viren Jain & H. Sebastian Seung & Winfried Denk, 2013. "Connectomic reconstruction of the inner plexiform layer in the mouse retina," Nature, Nature, vol. 500(7461), pages 168-174, August.
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    Cited by:

    1. Kyojiro N. Ikeda & Ilya Belevich & Luis Zelaya-Lainez & Lukas Orel & Josef Füssl & Jaromír Gumulec & Christian Hellmich & Eija Jokitalo & Florian Raible, 2024. "Dynamic microvilli sculpt bristles at nanometric scale," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    2. Ara Lee & Gihyun Sung & Sanghee Shin & Song-Yi Lee & Jaehwan Sim & Truong Thi My Nhung & Tran Diem Nghi & Sang Ki Park & Ponnusamy Pon Sathieshkumar & Imkyeung Kang & Ji Young Mun & Jong-Seo Kim & Hyu, 2024. "OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. H. G. Changela & Y. Kebukawa & L. Petera & M. Ferus & E. Chatzitheodoridis & L. Nejdl & R. Nebel & V. Protiva & P. Krepelka & J. Moravcova & R. Holbova & Z. Hlavenkova & T. Samoril & J. C. Bridges & S, 2024. "The evolution of organic material on Asteroid 162173 Ryugu and its delivery to Earth," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    4. Liang Wang & Ziyun Yang & Fudo Satoshi & Xavier Prasanna & Ziyi Yan & Helena Vihinen & Yaxing Chen & Yue Zhao & Xiumei He & Qian Bu & Hongchun Li & Ying Zhao & Linhong Jiang & Feng Qin & Yanping Dai &, 2024. "Membrane remodeling by FAM92A1 during brain development regulates neuronal morphology, synaptic function, and cognition," Nature Communications, Nature, vol. 15(1), pages 1-30, December.
    5. Martin Meschkat & Anna M. Steyer & Marie-Theres Weil & Kathrin Kusch & Olaf Jahn & Lars Piepkorn & Paola Agüi-Gonzalez & Nhu Thi Ngoc Phan & Torben Ruhwedel & Boguslawa Sadowski & Silvio O. Rizzoli & , 2022. "White matter integrity in mice requires continuous myelin synthesis at the inner tongue," Nature Communications, Nature, vol. 13(1), pages 1-18, December.

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