Bioimage analysis pipelines are a central component of modern biological research. Atthe same time, they are prone to structural, methodological, and organizational errorsthat can lead to non-reproducible results, biased measurements, or avoidableloss of time. This whitepaper describes typical pitfalls that are regularly observed in academicresearch environments and outlines concrete measures to prevent them. The focusis not on individual software tools, but on pipeline design, data integrity, andinstitutional frameworks.