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Human Cell Atlas

What is the Human Cell Atlas project

The Human Cell Atlas (HCA) project is international endeavour to create comprehensive reference maps of all cells in the human body. This collection of molecular single-cell maps will provide enormous insight into cellular biology, as well as providing a reference database from which automated cellular classification can be achieved. These efforts are partnered by other atlas-level projects, including the LifeTime initiative and the NIH Human BioMolecular Atlas Program (HubMAP) consortium.

Multi-modal single-cell technologies

Much of the data generated for the various single-cell and inflammatory atlas projects are generated using single-cell RNA sequencing (scRNAseq). In increasing frequency, datasets are being generated by incorporating multi-modal technologies, such as CITE-seq, where transcripts and antibodies on single-cells can be measured simultaneously. The presence of antibody labelling in these atlas datasets allows for direct integration between single-cell atlas datasets and independent high-dimensional cytometry datasets. An example of thise approach is described in Hao 2020, where CyTOF and CITE-seq data was integrated together using tools such as Azimuth.

Interfacing with atlas datasets using Spectre


  • Different challenges and requirements in analysis
  • Large cell volumes
  • Differences in QC and pre-processing
  • Differences in # of features, and implications for integration etc

Our approaches

  • Interface with data portals, or download data and do it manually…
  • Find common features
  • Re-render the resolvable populations in the reference dataset
  • Perform alignment
  • Perform label transfer

Further cell atlas resources and guidelines

In addition to direct interactions

seeking to help define the contribution of high-dimensional cytometry and imaging technologies to the HCA objectives (Czechowska et al. 2018, WS06: ‘Cytometry in the Era of the Human Cell Atlas’).