Whole-slide multiplex immuno-fluorescence (mIF) imaging is used to analyse tissue samples, enabling the study of complex spatial biology. In collaboration with the Immune Landscape Laboratory Platform from the CHUV, we have developed a mIF image analysis pipeline, fully integrated in the lab workflow, to routinely process tumor samples. The pipeline consists of a database and a web interface to help track sample processing in the lab, the IFQuant software to analyse mIF images and a web tool to explore and annotate the IFQuant results. The web tool enables zooming and panning of full-resolution images, displaying overlays of cell and tissue annotations and setting of marker signal thresholds. Results of the IFQuant pipeline are used as a basis for the spatial characterisation of the tumor microenvironment.

Preprint