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For the complete documentation index, see llms.txt. This page is also available as Markdown.

PhenoCycler Analysis

Resources for PhenoCycler analysis.

Commercial software tools: Visiopharm

Open-source software resources:

QuPath and CytoMap

  • A tutorial on how to use QuPath, CytoMap, and StarDist to segment cells, identify phenotypes with clustering or machine learning, and perform cell neighborhood analysis.

Additional open-source resources.

Data exploration tools

  • Seurat: R tools for spatial data exploration.

  • Squidpy: Python tools for spatial data exploration.

Data integration tools

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