Version 0.6.0

[0.6.0] — 2023-04-20

Added

• New output cell QC parameters avg_assignment_confidence, max_cluster_frac and lifespan
• Segmented cells are now saved to loom instead of TSV. To return an old behavior, use count-matrix-format="tsv"
• Minimal multi-threading (see README)

Removed

• iters and n-cells-init parameters were removed from the CLI shortcuts. To change them, use the config or --config.segmentation.iters and --config.segmentation.n_cells_init parameters (see 'Advanced configuration section in the readme').

Changed

• Breaking changes in config file structure and CLI
• Greatly improved responsiveness of the CLI and simplified installation process
• Major refactoring of the code
• Various performance improvements
• Faster and more precise algorithm for estimating boundary polygons. Now each cell has exactly one polygon in the output GeoJSON.
  • For method details see Awrangjeb, 2015, it's pretty similar.
  • Closes #15 and #41, potentially also #32 and #37.
• Using sparse PCA for NCV estimation on large datasets
• baysor segfree output is now fully compatible with loom v3 format
• Cells and NCVs now have IDs in the format {type}{run_id}-{cell_id}, where type is C for cells and V for NCVs, and run_id is a unique ID of Baysor run
• --save-polygons now works regardless of -p