This paper presents an image processing pipeline for electron cryo-tomography (cryo-ET) in RELION-5, which enables the analysis of cryo-ET data from unprocessed movies to automated atomic model building. The pipeline includes functionalities for importing unprocessed movies, tilt series alignment, CTF estimation, tomogram reconstruction, denoising, particle picking, and subtomogram averaging. The pipeline is designed with explicit metadata definitions to ensure interoperability with other software tools and to support further standardization. The metadata items describe tilt series, tomograms, and extracted particles, providing a framework for standardization in the cryo-ET field. The pipeline also includes tools for manual curation of images, particle picking, and automated alignment and classification. The pipeline is implemented in the free, open-source software RELION-5, which is compatible with various cryo-ET tools and provides a framework for further standardization. The pipeline has been tested on a benchmark dataset of five tomograms of virus-like particles, leading to a final map at 3.3 Å resolution. The results demonstrate the effectiveness of the pipeline in processing cryo-ET data and generating high-resolution structures. The paper also discusses the importance of standardization in cryo-ET image processing and the need for continued development of the pipeline to accommodate new techniques and tools. The pipeline is expected to improve the accessibility of cryo-ET data for newcomers to the field.This paper presents an image processing pipeline for electron cryo-tomography (cryo-ET) in RELION-5, which enables the analysis of cryo-ET data from unprocessed movies to automated atomic model building. The pipeline includes functionalities for importing unprocessed movies, tilt series alignment, CTF estimation, tomogram reconstruction, denoising, particle picking, and subtomogram averaging. The pipeline is designed with explicit metadata definitions to ensure interoperability with other software tools and to support further standardization. The metadata items describe tilt series, tomograms, and extracted particles, providing a framework for standardization in the cryo-ET field. The pipeline also includes tools for manual curation of images, particle picking, and automated alignment and classification. The pipeline is implemented in the free, open-source software RELION-5, which is compatible with various cryo-ET tools and provides a framework for further standardization. The pipeline has been tested on a benchmark dataset of five tomograms of virus-like particles, leading to a final map at 3.3 Å resolution. The results demonstrate the effectiveness of the pipeline in processing cryo-ET data and generating high-resolution structures. The paper also discusses the importance of standardization in cryo-ET image processing and the need for continued development of the pipeline to accommodate new techniques and tools. The pipeline is expected to improve the accessibility of cryo-ET data for newcomers to the field.