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

PLoS Biol. 2016 Jan 4;14(1):e1002340. doi: 10.1371/journal.pbio.1002340. eCollection 2016 Jan.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Image Processing, Computer-Assisted*
  • Microscopy
  • Software*

Grants and funding

This work was supported by Biocenter Finland, Biological Imaging Network (EJ), Academy of Finland (projects 131650 and 1287975; EJ) and the Integrative Life Science Doctoral Program of the University of Helsinki (MJ and DK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.