cellview

CellView: manage and explore single-cell measurement data.

cellview [OPTIONS] COMMAND [ARGS]...

Import measurements produced by the OMERO-Screen pipeline into a local DuckDB database, inspect projects, experiments and plates, and launch notebooks for interactive analysis.

Full --help output

Usage: cellview [OPTIONS] COMMAND [ARGS]...

  CellView: manage and explore single-cell measurement data.

  Import measurements produced by the OMERO-Screen pipeline into a local
  DuckDB database, inspect projects, experiments and plates, and launch
  notebooks for interactive analysis.

Options:
  --db PATH  Path to the DuckDB database file. Defaults to
             ~/.cellview/cellview.duckdb
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  clean          Clean up orphaned records in the database.
  curate         Curate tracked lineages through a replayable edit log.
  delete         Delete data from the database.
  edit           Edit project or experiment metadata.
  experiment     Show plates, channels and variables for experiment ID.
  explore        Launch a Jupyter notebook for interactive data exploration.
  export         Export the measurements for plate ID.
  import         Import data from a CSV file, an OMERO plate, or a screen.
  plate          Show summary, conditions and measurements for plate ID.
  project        Show experiments and plates for project ID.
  projects       List all projects with experiment counts.
  repair-tracks  Repair the tracked lineages of plate ID from...
  review-queue   Sample cells per well and write a review queue for the...
  template       Manage analysis notebook templates.

Options

--db: PATH: Path to the DuckDB database file. Defaults to ~/.cellview/cellview.duckdb
--version: Show the version and exit.

Commands

projects: List all projects with experiment counts.
project: Show experiments and plates for project ID.
experiment: Show plates, channels and variables for experiment ID.
plate: Show summary, conditions and measurements for plate ID.
import: Import data from a CSV file, an OMERO plate, or a screen.
edit: Edit project or experiment metadata.
export: Export the measurements for plate ID.
repair-tracks: Repair the tracked lineages of plate ID from segmentation flicker.
review-queue: Sample cells per well and write a review queue for the Track Review widget.
curate: Curate tracked lineages through a replayable edit log.
delete: Delete data from the database.
clean: Clean up orphaned records in the database.
explore: Launch a Jupyter notebook for interactive data exploration.
template: Manage analysis notebook templates.