Free Standalone Software/Tools/Plugins:

• Mantis-viewer: (2020)
  Image viewer ; Typ: free   MAC/Linux/Windows
  Mantis Viewer is an application developed by the Parker Institute for Cancer Immunotherapy for viewing and analyzing multi-channel pathology imaging, such as IHC, Vectra, MIBI, IMC, CODEX, or other technologies. 
  It has been designed to be highly performant and responsive when analyzing both large and small images and to support workflows with segmentation data.
   
• image_utils:  (2021)
  Type: free     Java script
  You can use image-utils to split up unsupported multi-image TIFFs into single channel TIFFs that can be analyzed by Mantis, until  Mantis is supporting this internally.

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Free SMC Data Analysis Software/Scripts/Pipelines:

CyCondor (2024) publication link
R/Docker based computational framework for the analysis of CyTOF, HDFC, SpectralFlow and CITE-seq data, 
covering not only all essential steps of cytometry data analysis but also including an array of downstream functions and tools to expand the biological interpretation of the data. 
The comprehensive suite of features of cyCONDOR, including guided pre-processing, clustering, dimensionality reduction, and machine learning algorithms.

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Free IMC Data Analysis Software/Scripts/Pipelines:

2024

• TRACERx-PHLEX: Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX. Nat Commun. 2024 Jun 15;15(1):5135. doi: 10.1038/s41467-024-48870-5.
  PHLEX is an automated and containerised Nextflow pipeline, manual assessment, programming skills or pathology expertise are not essential. 
  PHLEX offers an end-to-end solution in a growing field of highly multiplexed data and provides clinically relevant insights.
  The TRACERx-PHLEX pipeline is available on GitHub along with instructions on how to run it on the PHLEX test dataset: https://github.com/FrancisCrickInstitute/TRACERx-PHLEX.

2025

• Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem (2025): https://www.nature.com/articles/s41592-025-02817-w
  Giotto Suite can be downloaded from our GitHub page github.com/drieslab
• Vitessce: integrative visualization of multimodal and spatially resolved single-cell data. Nature Methods volume 22, pages 63–67 (2025). 
  The open-source software is available at http://vitessce.io.
• SPEX (Spatial Expression Explorer): A web-based analysis platform that employs modular analysis pipeline design, accessible through a user-friendly interface. (2025): https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf090/8244097
  SPEX is also available on GitHub: https://github.com/Genentech/spex

2026

• HARPY: Scalable analysis of whole slide spatial proteomics with Harpy. Bioinformatics. 2026, 42, btag122 (Python based)
  HARPY is also availabe on GitHub and tutorials can be found here.