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Open Source Tools for Biological Image Analysis.
Journal article

Open Source Tools for Biological Image Analysis.

  • Guiet R Faculty of Life Sciences (SV), BioImaging and Optics Platform (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
  • Burri O Faculty of Life Sciences (SV), BioImaging and Optics Platform (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
  • Seitz A Faculty of Life Sciences (SV), BioImaging and Optics Platform (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. arne.seitz@epfl.ch.
  • 2019-08-22
Published in:
  • Methods in molecular biology (Clifton, N.J.). - 2019
Image analysis
ImageJ
Interoperability
Open source software
Algorithms
Biological Science Disciplines
Image Processing, Computer-Assisted
Information Dissemination
Microscopy
Reproducibility of Results
Software
English Visiting the Bio Imaging Search Engine (BISE) (Bio, BISE, Engine, http://biii.eu/, Imaging, Search) website at the time of writing this article, almost 1200 open source assets (components, workflows, collections) were found. This overwhelming range of offer difficults the fact of making a reasonable choice, especially to newcomers. In the following chapter, we briefly sketch the advantages of the open source software (OSS) particularly used for image analysis in the field of life sciences. We introduce both the general OSS idea as well as some programs used for image analysis. Even more, we outline the history of ImageJ as it has served as a role model for the development of more recent software packages. We focus on the programs that are, to our knowledge, the most relevant and widely used in the field of light microscopy, as well as the most commonly used within our facility. In addition, we briefly discuss recent efforts and approaches aimed to share and compare algorithms and introduce software and data sharing good practices as a promising strategy to facilitate reproducibility, software understanding, and optimal software choice for a given scientific problem in the future.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/69504
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