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

• MARIO

• STvEA

• GLUER