Cells2Stats workflow

The cells2stats-nf workflow by Element Biosciences is a Nextflow workflow that generates cytoprofiling data from cytoprofiling run data produced by AVITI Systems.

This workflow runs as part of ElemBio Cloud, but can also be used independently and reproducibly in any Nextflow environment (local or cloud-based).

Workflow summary

Description

Converting raw images is the necessary first step to view cytoprofiling data in CytoCanvas™. This single step pipeline uses the Cells2Stats Software to process cytoprofiling data.

Workflow diagram

Release notes

The workflow repository is maintained on GitHub, where you can find tags, release notes, and the latest updates.

Inputs

Input	Description	Constraints
Run Directory	An AVITI24 System cytoprofiling run directory.	Required
Cytoprofiling Run Manifest	By default, the run manifest in the output run directory is used. If required, an alternate run manifest can be provided to overwrite cells and pass metadata.	Optional
Cell Segmentation	If required, an alternate cell segmentation file set instead of the segmentation provided in the run directory.	Optional
Parameters	In addition to the dataset, parameters can tune the output.	Optional

Output

Cells2Stats outputs cytoprofiling metrics and visualization data for CytoCanvas. Depending on the parameters used, the output directory may be different. See Cells2Stats outputs for specific details of output files.

Representative view of Cells2Stats output

s3://output-bucket/analysis
└── wfr_6744a40907f338871a96cd9b
    ├── BaseCalling/
    ├── CellSegmentation/
    ├── Cytoprofiling/
    │   └── 20260519T195105Z/
    │       ├── RunManifest.json
    │       ├── RunManifest.csv
    │       ├── RunParameters.json
    │       ├── Panel.json
    │       ├── AverageNormWellStats.csv
    │       ├── RawCellStats.csv
    │       ├── RawCellStats.parquet
    │       ├── RunStats.json
    │       ├── multiqc_report.html
    │       ├── Versions.json
    │       ├── Wells/
    │       │   └── WellXX/BXX/
    │       │       └── LXRXXCXXS1_barcodes.parquet
    │       ├── CellSegmentation/
    │       │   └── WellXX/
    │       │       ├── LXRXXCXXS1_Cell.tif
    │       │       └── LXRXXCXXS1_Nuclear.tif
    │       └── SpatialData/
    │           ├── cyto.viz
    │           ├── RunName.zarr-index.json.gz
    │           ├── RunName.zarr.zip
    │           ├── cell_shapes_global.parquet
    │           ├── nuclear_shapes_global.parquet
    │           └── points_global.parquet
    ├── Ebitt/
    ├── Projection/
    ├── Thumbnails/
    ├── Panel.json
    ├── RunAnalysisFilesUploaded.json
    ├── RunManifest.csv
    ├── RunManifest.json
    ├── RunParameters.json
    ├── RunStats.bin
    └── RunUploaded.json

Input parameters

Parameter	Type	Results
batch	boolean	Applies the --batch option with the supplied value to limit which batches are used.
max_unassigned	integer	Applies the --max-unassigned option with the supplied value to limit reported unassigned sequences.
skip_cellprofiler	boolean	Applies the --skip-cellprofiler option to skip generating morphology features.
no_error_on_invalid	boolean	Applies the --no-error-on-invalid option to skip invalid files.
tile	string	Applies the --tile option with the supplied value to limit which tiles are used.
well	string	Applies the --well option with the supplied value to limit which wells are used.