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CHANGELOG.md

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[0.6.2] — 2023-08-15

Fixed

  • Fixed wrong parameter interpretation in neighborhood_count_matrix()
  • Fixed incompatibility with julia-1.9 (#78)
  • Fixed boundary_polygons_from_grid error (#82)
  • Fixed a problem with huge integers in cell ids (#83)

[0.6.1] — 2023-05-11

Fixed

  • Fixed a bug with prior segmentation loading
  • Fixed a bug with compartment genes

[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.
  • 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

[0.5.2] — 2022-06-29

  • Fixed some package versions, dependencies should cause fewer bugs now
  • Fixed some bugs
  • Fixed random seed for all CLI runs
  • Adjusted some CLI parameters
  • Added segfree run option to extract NCV vectors

[0.5.1] — 2021-12-01

Changed

  • Slightly optimized compilation time
  • Minor updates of core formulas

Added

  • CLI parameter no-ncv-estimation to disable estimation of NCVs

[0.5.0] — 2021-06-03

Changed

  • scale-std now can be specified from CLI parameters
  • Several bugs fixed
  • Allow missing genes in the input data
  • Updates in the core algorithm
  • All diagnostic plots were updated

Added

  • exclude-genes option that removes genes from the data frame before segmentation.
  • Segmentation of compartments based on the list of compartment-specific genes
  • Using information about compartment per molecule in the segmentation algorithm when available
  • 3D segmentation

Removed

  • The data can not be split by frames anymore. This functionality didn't work well previously and was hard to maintan.

[0.4.3] — 2021-04-06

Changed

  • Fixed the CLI installation bug
  • More information in logging
  • Better initialization for molecule clustering. This should improve cell separability a lot!
  • Some memory optimization
  • Fixed plotting performance by moving to Makie.jl

Added

  • Estimating scale when prior segmentation is provided as a CSV column
  • Added the option --save-polygons=GeoJSON to save cell boundary polygons in the GeoJSON format

[0.4.2] — 2020-11-26

Changed

  • Fixed Makefile julia version
  • Improved polygon visualization
  • Regressed to Plots 1.6.0 because of the performance issues
  • Fixed docker build
  • Small bug fixes
  • min-molecules-per-segment parameter is working now
  • Fixed visualization of prior segmentation

[0.4.1] — 2020-10-30

Added

  • Added travis config
  • Saving NCV colors to the ncv_color field of segmentation.csv

Removed

  • Dropped support for julia < 1.5

Changed

  • Updated dependencies
  • find_grid_point_labels_kde now preserves label ids
  • Fixed docker build
  • Added ImageMagick dependency to fix problems with DAPI prior