On the reproducibility of biological image workflows by annotating computational results automatically

Abstract

When microscopy image data are stored and processed, the corresponding workflow is typically carried out by treating storing and processing separately. In many laboratories, it is common to store data on one computing system and process data on another system. This separation of storing and processing data has a negative impact on the traceability of results, and thus on reproducibility, as information has to be manually transferred between these systems. We resolve this difficulty by introducing a novel system called Omero Processing Extension (OPE) that generates a description of the execution of a workflow and annotates the calculation results automatically. This way, OPE establishes a bridge between storage and processing. Plugins provide support for version control to link program sources with the executed workflow. In addition, a web interface provides access to OPE improving the reproducibility with minimal overhead for the user.

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