jicbioimage: a tool for automated and reproducible bioimage analysis

Clicks: 285
ID: 134735
2016
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Abstract
There has been steady improvement in methods for capturing bioimages. However analysing these images still remains a challenge. The Python programming language provides a powerful and flexible environment for scientific computation. It has a wide range of supporting libraries for image processing but lacks native support for common bioimage formats, and requires specific code to be written to ensure that suitable audit trails are generated and analyses are reproducible. Here we describe the development of a Python tool that: (1) allows users to quickly view and explore microscopy data; (2) generate reproducible analyses, encoding a complete history of image transformations from raw data to final result; and (3) scale up analyses from initial exploration to high throughput processing pipelines, with a minimal amount of extra effort. The tool, jicbioimage, is open source and freely available online at http://jicbioimage.readthedocs.io.
Reference Key
olsson2016peerjjicbioimage: Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Tjelvar S. G. Olsson;Matthew Hartley
Journal pediatrics
Year 2016
DOI
10.7717/peerj.2674
URL
https://peerj.com/articles/2674/
Keywords
Image processing automation reproducibility provenance bioimage analysismedicine

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