# PhenoCycler Analysis Commercial software tools: [Visiopharm](https://visiopharm.com/visiopharm-digital-image-analysis-software-features/phenotyping-multiplexed-images/) Open-source software resources: [QuPath and CytoMap](https://akoyabio-my.sharepoint.com/:w:/p/gcarlson/EaY3tNbcRoJJlHXzj83xc5UBNW5WNNSUOmVbhXCMSBn-Ng?e=4WTFfW) * 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](https://satijalab.org/seurat/articles/spatial_vignette_2.html#human-lymph-node-akoya-codex-system-1): R tools for spatial data exploration. * [Squidpy](https://squidpy.readthedocs.io/en/stable/index.html): Python tools for spatial data exploration. Data integration tools * [MARIO](https://github.com/shuxiaoc/mario-py/blob/main/tutorials/mario-py-tutorial-BM.ipynb) * [STvEA](https://github.com/CamaraLab/STvEA) * [GLUER](https://github.com/tanlabcode/GLUER) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.codex.bio/codex/phenocycler-analysis.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.