# 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)