Nature Methods – Open Source – Bioimage Informatics

July 17, 2012

 This month’s issue of Nature Methods has a focus on bioimage informatics:

“Explosive growth in the size and complexity of microscopy-based imaging data and the need to extract more quantitative data from it increasingly requires sophisticated image acquisition and analysis methods and software tools. A collection of articles discusses the role of bioimage informatics in microscopy, specific tools that are available, and the challenges and opportunities in the field.”

Among the many interesting articles of this issue, one includes a review of  biological imaging software tools, which includes – among others – ITK and VTK.

The review walks through each computational step that biologists encounter when dealing with digital images, the inherent challenges, and overall status of available software for bioimage informatics, with a focus on open-source options:

workflow figure(Nature Methods 9, 697–710 (2012) doi:10.1038/nmeth.2084)

The major topics in this review include:

  • Image Acquisition
  • Image Storage
  • Image Analysis and Visualization
  • Bioimaging Libraries and Toolkits
  • Machine Learning
  • Workflow Systems

The full paper is available online.

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