Single cell and spatial transcriptomics illuminate complementary features of tissues. However, the online dissemination and exploration of multi-modal datasets is challenging. Here, I will introduce our WebAtlas pipeline for user-friendly sharing and interactive navigation of integrated datasets. WebAtlas unifies commonly used atlassing technologies into the cloud-optimized Zarr format and builds on Vitessce to enable remote data navigation. I will present a use-case of WebAtlas on the developing human lower limb to cross-query cell types and genes across single cell, sequencing- and imaging-based spatial transcriptomic data. The WebAtlas pipeline and multi-modal data portals can be accessed at Human Developmental Cell Atlas.