BellaVista: Open-Source Visualization for Imaging-Based Spatial Transcriptomics

Imaging-based spatial transcriptomics can reveal gene expression in situ by locating and identifying individual RNA molecules at subcellular resolution. These datasets typically contain an abundance of information that when analyzed appropriately can reveal tissue organization across scales from molecules to entire organs. However, there is currently a lack of simple open-source tools that facilitate visualization, quality control, and custom spatial analysis. Here we introduce BellaVista, a lightweight open-source tool for interactive visualization and exploration of imaging-based spatial transcriptomics data. BellaVista natively supports data from Xenium (10x Genomics), MERSCOPE (Vizgen), and custom MERFISH platforms. By providing a simple means for simultaneous visualization of images, transcripts, and cell segmentation boundaries, we anticipate that BellaVista will accelerate accessibility, exploration and discovery in the rapidly expanding field of spatial biology. BellaVista is available at https://github.com/pkosurilab/BellaVista.