Taylor-CCB-Group/SpOOx: First release

Version: 1.0.0
Release Date: 6th September 2023

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.

1. Automated Processing: SpOOx automatically processes MCD image files, which are generated by the Fluidigm Hyperion Imaging System.
2. Image Processing with imctools: Integration with imctools provides advanced image processing capabilities.
3. Segmentation with DeepCell: Utilizes DeepCell for accurate and efficient image segmentation.
4. Custom Scripts for Data Analysis: Extracts marker intensities, conducts quality control, and performs cell clustering to support cell phenotyping.
5. Spatial Statistical Analysis: Includes innovative procedures for novel spatial statistical analysis.

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.

• 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.

• Tested to work on Linux HPC. Untested on Windows / macOS.

We value your feedback. If you have any questions, suggestions, or encounter any issues, please report them in Issues on GitHub.