What question did this study set out to answer?

The aim is to identify common errors in bioimage analysis pipelines and provide solutions to avoid them.

February 6, 2026Open Access

Common Pitfalls in Bioimage Analysis Pipelines and How to Avoid Them

Key Points

The aim is to identify common errors in bioimage analysis pipelines and provide solutions to avoid them.
Identified typical pitfalls in bioimage analysis within academic research environments.
Analyzed structural, methodological, and organizational errors.
Proposed concrete measures for improving pipeline design and data integrity.
Highlighted the non-reproducibility of results caused by common errors.
Described the impact of biased measurements on research outcomes.
Recommended strategies to streamline bioimage analysis workflows and reduce errors.

Abstract

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.

Connected Papers

Building similarity graph...

Analyzing shared references across papers

Discussion

Cite this study

Jan Brocher (Wed,) studied this question.

www.synapsesocial.com/papers/698586498f7c464f2300a592 — DOI: https://doi.org/10.5281/zenodo.18485502

Common Pitfalls in Bioimage Analysis Pipelines and How to Avoid Them

Key Points

Abstract

Citation Network

Connected Papers

Discussion

Cite this study

Authors

Actions

Institutions

References and Citations

Citation Network

Connected Papers

Discussion