Multimodal Annotation Tutorials

Our friends at the Chan Zuckerberg San Francisco BioHub Data Science Team have been developing methods to help annotate multimodal data. While not supported by the Chan Zuckerberg CELLxGENE team, we wanted to make their learning available to the broader community through these tutorials and trainings they have put together. This is an ongoing effort, so please check back to see the latest modalities available.

Questions, feedback, or requests? Reach out to Yang Joon Kim at

exCELLxGENE Tutorial and Download Link


A fork of CZ CELLxGENE Annotate, this tool has additional features to help you annotate and explore your data, such as Leiden clustering (with user-defined resolution), subsetting and re-embedding for a small population of cells in 2D embedding, Sankey diagrams to visualize the hierarchy of clustering, data preprocessing (QC, log-normalization, dimensionality reduction, computing UMAP, etc.), and more.

Find the link to download and install the tool here:

Annotating Spatial Transcriptomics Data Tutorial and Download Link

Coming soon!

Annotating CITE-seq Data Tutorial and Download Link

Coming soon!