SpOOx - Spatial Omics Oxford Analysis Pipeline Release Notes Version: 1.0.0 Release Date: 6th September 2023 Overview: SpOOx is a state-of-the-art pipeline developed in close collaboration with clinicians, computational biologists, laboratory scientists, and mathematicians, offering a comprehensive analysis of spatial proteomics data. Features: Automated Processing: SpOOx automatically processes MCD image files, which are generated by the Fluidigm Hyperion Imaging System. Image Processing with imctools: Integration with imctools provides advanced image processing capabilities. Segmentation with DeepCell: Utilizes DeepCell for accurate and efficient image segmentation. Custom Scripts for Data Analysis: Extracts marker intensities, conducts quality control, and performs cell clustering to support cell phenotyping. Spatial Statistical Analysis: Includes innovative procedures for novel spatial statistical analysis. Recommendation: For an enhanced user experience and a more detailed analytics approach, we strongly recommend uploading the outputs of SpOOx to our comprehensive analytics and visualisation platform: MDV Multi-Dimensional View. Changelog: Initial Release: First version of the SpOOx pipeline released to the public. Introduced automated processing of MCD image files. Integrated with imctools and DeepCell for image processing and segmentation respectively. Introduced custom scripts for detailed data analysis. Embedded novel spatial statistical analysis procedures. Known Issues and Limitations: Tested to work on Linux HPC. Untested on Windows / macOS. Feedback and Support: We value your feedback. If you have any questions, suggestions, or encounter any issues, please report them in Issues on GitHub.