Learning how proteins are organized into different tissues is crucial for understanding their functionality. Since its inception in 2003, The Human Protein Atlas (HPA) database has embarked on the ambitious mission of mapping all human proteins in tissues and cells. This invaluable resource provides an extensive collection of single-plex immunohistochemistry tissue
images, as well as advanced 6-plex Opal immunofluorescence staining, to the scientific community.

In 2024, significant contributions were made by multiplexing over 40 proteins across 46 normal tissues and 20 different cancers, further enhancing the ability to explore protein distribution and interactions on a broader scale. However, the increased multiplexing of proteins in larger tissues presents challenges related to data analysis complexity. To address this, the Lundberg Lab at Stanford developed an open-source programming pipeline platform with a graphical user interface (GUI) called PIPEX. PIPEX incorporates the necessary steps to translate the protein information contained within the images into quantitative metrics, facilitating improved analysis and interpretation of data.