Multiplexed whole slide imaging allows to acquire from 6 to 60 markers at the scale of the slide. The acquired images enable to study the relationships between a multitude of different cell types and their environment. However, the analysis of such large data requires expertise that most biologists lack. The goal of the workshop is to present a workflow with open-source software to process multiplexed whole slide images. More precisely, QuPath will be used to visualize whole slide images, to segment nuclei with a deep learning approach (Stardist) and to export measurements associated to cells. Cytomap will then be used to perform a dimensionality reduction and to identify the different cell types with an unsupervised clustering algorithm. The workflow will be demonstrated on 6-7 plexed images acquired during another workshop (Multiplexing and whole slide imaging for a quantitative histopathologic analysis). Each step of the workflow will be presented in details so that participants can analyze the images during the workshop that will take place in a computer room, but participants can also bring their own computer as long as QuPath and Cytomap are installed.