OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry

Imaging Mass Cytometry (IMC) enables spatially resolved single-cell proteomics, but fragmented data analysis tools limit reproducibility. We present OpenIMC, an open-source platform consolidating IMC workflows into a cohesive environment. OpenIMC integrates visualization, preprocessing, segmentation, feature extraction, phenotyping, and spatial analysis. Accessible via graphical and command-line interfaces sharing a backend, the platform ensures consistent execution. Built for scalability and reproducibility, OpenIMC automatically records analytical parameters and enables sharing of complete sessions. Case studies analyzing blood-derived cells and tissue slices validate the software platform by recovering known phenotypes and structural organization. OpenIMC lowers technical barriers, supporting rigorous, scalable single-cell and spatial proteomics.