Recent advancements in microscopy technology have revolutionized our ability to routinely acquire large, multi-dimensional image datasets. However, gaps remain in the effective analysis of this data, primarily due to a lack of computational skills among researchers. This often results in a reliance on qualitative, manual image assessments, which lack the precision, reproducibility, and scalability that automated, quantitative analysis can provide. To bridge this gap, this two-day workshop is designed to empower microscopists and researchers with the necessary skills and tools to confidently analyse their data. Under the instruction of experienced core facility staff from the Francis Crick Institute and King’s College London, participants will be introduced to open-source tools such as FIJI and napari, and will be introduced to methodologies for automating their image analyses, thus enhancing research precision, efficiency, and reproducibility.