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Optional Arguments

The following arguments are optional additions to a Cells2Stats execution command.

--batch​

Use --batch or -b to specify which batches of B01-B07 to use.

cells2stats /input -b B01
cells2stats /input --batch B01

The following example includes B01, B02, and B03.

cells2stats /input -b B01,B02,B03
cells2stats /input --batch B01,B02,B03

--cellprofiler​

Use --cellprofiler or -c to specify the path to the CellProfiler utility to use. This is an external dependency used to generate morphology metrics. If you do not want to specify a CellProfiler utility and do not have CellProfiler installed, run with [--skip-cellprofiler](#--skip-cellprofiler).

cells2stats /input -c /path/to/cellprofiler
cells2stats /input --cellprofiler /path/to/cellprofiler

--error-on-missing​

Use --error-on-missing or -m to make an execution terminate when a non-critical file is missing, rather than the default behavior of skipping the file and continuing the execution.

cells2stats /input --error-on-missing

--help​

Use --help or -h to display the usage statement for Cells2Stats.

cells2stats -h
cells2stats --help

--input-remote​

Use --input-remote or -i to set the rclone remote name that points to the input files.

cells2stats /input --input-remote '<input-name>'

--log-level​

Use --log-level or -l to specify the minimum level required to log an event. Use one of the following valid values. The default value is INFO.

  • INFO
  • DEBUG
  • WARNING
  • ERROR
cells2stats /input -l DEBUG
cells2stats /input --log-level WARNING

--max-unassigned​

Use --max-unassigned or -u to limit the number of unassigned sequenced reported, from 1-10000 sequences. By default, the value is set to 30.

cells2stats /input -u 100

--no-error-on-invalid​

Use --no-error-on-invalid or -n to skip non-critical files that Cells2Stats identifies as invalid.

cells2stats /input --no-error-on-invalid

--num-threads​

Use --num-threads or -j to specify the number of threads to use for processing, with a minimum value of 1 and a maximum value that depends on your system. The default value is 1.

cells2stats /input -j 8
cells2stats /input --num-threads 8

--output​

Use --output or -o to specify the location to save the output. The default is the INPUT_RUN_DIRECTORY/Cytoprofiling/<timestamp> folder. .

cells2stats /input -o /output

--output-remote​

Use --output-remote to set the rclone remote name that points to the output files.

cells2stats /input -o /output --output-remote '<output-name>'

--panel​

Use --panel or -p to set the path to the panel file. The file path can direct to a local or remote location.

cells2stats /input -o /output -p /panel
cells2stats /input -o /output --panel /input/<corrected_panel_filename>.json

--python​

Use --python or -P to set the path to set the python version to execute.

cells2stats /input -o /output -P /path/to/python/version
cells2stats /input -o /output --python /path/to/python/version

## --run-manifest

Use `--run-manifest` or `-r` to define the location of an alternate run manifest for the execution instead of the `RunManifest.csv` file output by the instrument. For information on corrected run manifests, see the [Run Manifest Documentation](/docs/run-manifest/#corrected-run-manifest).

```bash
cells2stats /input -o /output -r /input/<corrected_manifest_filename.csv>
cells2stats /input -o /output --run-manifest /input/<corrected_manifest_filename.csv>

--segmentation​

Use --segmentation or -S to pass in a directory of alternative cell segmentation masks. To learn more about how to create a directory of cell segmentation masks, see our Resegmentation Using Python tutorial and see the expected format of an Alternative Cell Segmentation Directory.

cells2stats /input -o /output --segmentation /input/<path-to-alternative-cell-segmentation-directory>
cells2stats /input -o /output -S /input/<path-to-alternative-cell-segmentation-directory>

--skip-cellprofiler​

Use --skip-cellprofiler to skip the execution of CellProfiler. This saves execution time and allows you to run Cells2Stats without a CellProfiler dependency. When you skip the execution of CellProfiler, morphology features will not be generated in your RawCellStats.csv or RawCellStats.parquet files.

cells2stats /input  --skip-cellprofiler
cells2stats /input  -s

--tile​

Use --tile or -t to specify the tiles to run on. The argument uses regex to identify the selected tiles.

cells2stats -t L1R05C03S1
cells2stats --tile L1R05C03S1

The following example includes the subset of tiles in Lane 1 L1R..C..S.

cells2stats --tile L1R..C..S.

--version​

Use --version or -v to display the current version of Cells2Stats. Cells2Stats logs the version at the start of any execution on the command line and in the log file.

cells2stats -v
cells2stats --version

--visualization​

Use --visualization or -V to create CytoCanvas input files as part of the Cells2Stats output. Use this command if you have a directory of alternative segmentation masks for which you would like to perform target to cell assignment and regenerate all cell statistics files as well as visualization files. Otherwise, you likely want to use --visualization-only.

cells2stats /input -V -S /input/<path-to-alternative-segmentation-masks>
cells2stats /input --visualization -S /input/<path-to-alternative-segmentation-masks>

--visualization-only​

Use --visualization-only or -O to create CytoCanvas input files as the Cells2Stats output without performing target to cell assignment or regenerating cell statistics files. Use this command if you want to prepare your original run output for visualization in CytoCanvas.

cells2stats /input -O
cells2stats /input --visualization-only

--well​

Use --well or -w to specify which well of A1-F2 to use for a run using a 12-well consumable.

cells2stats -w A1
cells2stats --well A1

The following example includes wells A1, A2, and B1.

cells2stats -w A1,A2,B1
cells2stats --well A1,A2,B1
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