Discussion

State-of-the-art high-throughput microscopy calls for software solutions that can handle huge volumes of heterogeneous image data. These kinds of software solutions have to fulfill an extensive range of requirements (e.g. image analysis, machine learning, statistics, and visualization) and yet still be easy to use for the non-expert. A large number of monolithic and highly task-oriented platforms is available for analyzing biological image data. However, in view of the diverse nature of present problems, it is often necessary to integrate several applications. This involves going through many manual, time-consuming and error-prone steps, which are hard to document and therefore incomprehensible to others. Therefore, integrative workflow systems become increasingly popular. KNIME is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform designed to handle large amounts of heterogeneous data. As an integration platform, KNIME directly combines functionality from several different tools and domains. The KNIME Image Processing Extension enhances KNIME by providing algorithms and data-structures to process and analyze images. Combined with other existing KNIME extensions, non-experts can easily compose complex domain comprehensive workflows to process images on a large scale. Not wishing to reinvent the wheel, KNIME Image Processing integrates with ImageJ, OMERO, ClearVolume and CellProfiler, among others.