Human Biomolecular Atlas Program (HuBMAP) Usage of OME-TIFF

The Human Biomolecular Atlas Program (HuBMAP) is dedicated towards mapping the human body at the single-cell level. Forty-two contributing sites, including tissue mapping centers and a data core, work with a variety of experimental assays on tissue samples from 31 organs throughout the human body. As part of the data submission process, tissue mapping centers working with modalities involving histology and spatial transcriptomics locally convert varying lab instrument imaging formats into OME-TIFF images using tools like Bio-Formats. Using a central analysis pipeline, those OME-TIFF images submitted as part of HuBMAP datasets are converted to OME-TIFF pyramids for portal display using a software called Vitessce. HuBMAP's usage of OME-TIFF exemplifies how data repositories and knowledge bases can use the file format to standardize and visualize imaging data.