Version 2.0.14 was released on Sep 21, 2018 (release notes).

Loom is an efficient file format for large omics datasets. Loom files contain a main matrix, optional additional layers, a variable number of row and column annotations, and sparse graph objects. Under the hood, Loom files are HDF5 and can be opened from many programming languages, including Python, R, C, C++, Java, MATLAB, Mathematica, and Julia.

Key features:

  • Single file that can be moved around
  • Metadata travels with the main data
  • Data, clustering, layout, annotation stored together
  • Efficient random access
  • Automatic, on-the-fly compression
  • Out-of-memory data processing
  • Open source, BSD license


Additional resources

Many popular packages support Loom files out of the box, including scanpy from Fabian Theis lab, SCope from Stein Aerts lab, LoomExperiment from Bioconductor, and scVI from Nir Yosef's lab.