# cellview


CellView: manage and explore single-cell measurement data.


``` bash
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.


<span class="gd-details-chevron" aria-hidden="true"></span>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.](../../reference/cli/projects.md)

`project`  
[Show experiments and plates for project ID.](../../reference/cli/project.md)

`experiment`  
[Show plates, channels and variables for experiment ID.](../../reference/cli/experiment.md)

`plate`  
[Show summary, conditions and measurements for plate ID.](../../reference/cli/plate.md)

`import`  
[Import data from a CSV file, an OMERO plate, or a screen.](../../reference/cli/import.md)

`edit`  
[Edit project or experiment metadata.](../../reference/cli/edit.md)

`export`  
[Export the measurements for plate ID.](../../reference/cli/export.md)

`repair-tracks`  
[Repair the tracked lineages of plate ID from segmentation flicker.](../../reference/cli/repair_tracks.md)

`review-queue`  
[Sample cells per well and write a review queue for the Track Review widget.](../../reference/cli/review_queue.md)

`curate`  
[Curate tracked lineages through a replayable edit log.](../../reference/cli/curate.md)

`delete`  
[Delete data from the database.](../../reference/cli/delete.md)

`clean`  
[Clean up orphaned records in the database.](../../reference/cli/clean.md)

`explore`  
[Launch a Jupyter notebook for interactive data exploration.](../../reference/cli/explore.md)

`template`  
[Manage analysis notebook templates.](../../reference/cli/template.md)