Vizbi Poster: Web based Visual Exploration of the Mouse Liver at Single-Cell Resolution with Vizgen MERFISH Open Data Set
Abstract:
MERFISH (multiplexed error-robust fluorescence in situ hybridization) is a novel single-cell transcriptomics technology that captures spatial gene expression patterns across whole tissue slices with sub-cellular resolution.1 However, it can be difficult for researchers to visually analyze and explore the large amounts of data (e.g., image, transcriptomic) generated by a typical MERFISH experiment and turn these data into meaningful insights. To help address these issues, we developed an open web based visualizer and opensource Google Colab notebook that allow users to visually explore the recently released Vizgen MERFISH Mouse Liver Map MERFISH dataset.<sup<2,3 Our Web Vizualizer allows users to visually explore the expression of hundreds of millions of transcripts from 347 genes across 350,000 single cells in a single tissue slice as well as overlay cell segmentation boundaries4 and high-resolution background images. Our Google Colab notebook demonstrates how to perform single-cell clustering and spatial analysis of cell types in the mouse liver. These tools and open data are freely available to the research community via the Vizgen website.