title: jicbioimage: a tool for automated and reproducible bioimage analysis.
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.
authors.affiliation: Computational Systems Biology, John Innes Centre , Norwich, UK , United Kingdom.
authors.forename: Tjelvar S G
authors.initials: TS
authors.lastname: Olsson
authors.affiliation: Computational Systems Biology, John Innes Centre , Norwich, UK , United Kingdom.
authors.forename: Matthew
authors.initials: M
authors.lastname: Hartley
keywords: Audit trail; Automation; Bioimage analysis; Image processing; Provenance; Rapid iteration; Reproducibility