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Introduction

Cells2Stats processes cytoprofiling data to generate detailed statistics and outputs that enable downstream analysis, including visualization using the CytoCanvas tool. This tool is designed for use with Element Biosciences AVITI24 systems and provides flexible options for handling both local and cloud-based data storage.

The software offers the following features:

  • Cytoprofiling metrics: Generation of comprehensive morphology and intensity metrics, with support for CSV and Parquet file formats.
  • Visualization-ready outputs: Creation of files compatible with CytoCanvas for visualization of cytoprofiling results.
  • Customizable execution: Flexible support for local and cloud environments, including AWS S3, Google Cloud Storage, and rclone-compatible providers.
  • Extensive optional arguments: Tailor execution commands with options such as specifying alternative cell segmentation directories and running in visualization-only mode.

Setting up a Cloud Cells2Stats Execution Environment​

While cytoprofiling run data can be reanalyzed by Cells2Stats in any local or cloud compute environment, Element provides options to automate cell statistic generation using ElemBio Cloud. The following cloud providers can be used to facilitate reanalyzing cell statistics and generating CytoCanvas visualization files on run complete in ElemBio Cloud:

Software Workflow​

Cells2Stats is executed via the command line and can be run using a Docker container or a static binary. The workflow involves the following steps:

  1. Input preparation:

    • Files are typically generated by an AVITI24 run and structured for input to Cells2Stats.
    • If needed, you can specify an alternative directory of cell segmentation masks, an alternative Panel.json, or an alternative Run Manifest.

  2. Execution:

    • Cells2Stats processes the input data, performing cell assignment and feature extraction in order to generate cell statistics including target counts and morphology features per cell. Cells2Stats also prepares run outputs for use with CytoCanvas for visualization.
    • Optional arguments allow customization of processing, such as specifying batches, wells, whether to generate morphology features with CellProfiler, whether to generate files for CytoCanvas, and more.

  3. Output generation:

  • Cells2Stats produces output files and copies them into the output location.
  • Output generation can include target metrics, morphology features, and CytoCanvas visualization files depending on optional arguments.

Outputs​

Cells2Stats produces a wide range of output files and directories, including:

  • RawCellStats.csv and RawCellStats.parquet: Per-cell target and morphology metrics.
  • AverageNormWellStats.csv: Normalized target metrics for each well.
  • RunStats.json: Summary of execution and general run statistics.
  • Logs (Cells2Stats.log and Visualization.log) details of execution.
  • Visualization files (cyto.viz and additional folders) for CytoCanvas.

For detailed descriptions of all input and output files, see the Inputs and Outputs documentation.

License Agreement​

Use of Cells2Stats is subject to the license agreement available on the Element Biosciences website.

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