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Cells2Stats Release Notes

v1.3.0​

July 30, 2025

Improvements​

  • Support is now available for cytoprofiling runs that are executed with the new Teton™ Custom Screen cartridge and three assay options that are available in AVITI™ OS 3.4.0.
  • Added a new AntibodyScreeningKitReport.csv file for Teton Custom Screen runs, that includes cell, control, and target antibody information. This file can be used when evaluating the run to review the target counts or negative control counts per cell (normalized values).
  • Support is now available for cytoprofiling runs that are executed with the new Teton Atlas™ cartridge in AVITI OS 3.4.0.
  • When Target Cell Assignment is enabled for any target in the run, TargetCounts.json, TargetCellAssignment.csv, and TargetCellAssignmentManifest.json output files are included.
  • Added new optional arguments:
    • --bases2fastq, -B: The path to Bases2Fastq binary that is used for fastq generation during Optical Poolded Screen analysis.
    • --bowtie: The path to bowtie (v1) binary that is used in Optical Pooled Screen analysis.
    • --bowtie-build: The path to bowtie build binary that is used in Optical Pooled Screen analysis.
    • --samtools: The path to samtools binary that is used in Optical Pooled Screen analysis.
    • --tca-manifest, -M: The local or remote path to target cell assignment manifest. Must have CSV or JSON extension.
    • --skip-html-report, -H: Used to skip the creation of MultiQC HTML reports.
  • A new MultiQC HTML report, which is an interactive HTML quality control summary that is generated from the RunStats.json summary, can now be generated. This report also supports combining results of other bioinformatics tool outputs across one or more runs into a single report, which provides an efficient method to compare results across tools or runs.
  • Added new fields to the RunStats.json file for improved spatial analysis and to support Teton Atlas and Teton Custom Screen cytoprofiling run types.
  • Added new columns to the RawCellStats file.
  • Updated the visualization output files to improve the CytoCanvas™ display:
    • RawCellStats.parquet copies into the visualization output directory to support Optical Pooled Screen run visualization in CytoCanvas 1.2.0-beta.
    • Included image information in the cyto.viz file to support Optical Pooled Screen run visualization in CytoCanvas.
  • New segmentation boundary smoothing algorithm to improve smoothing and reduce jagged edges.

v1.2.0​

April 8, 2025

Improvements​

  • Enhanced the RawCellStats file - Added the following fields for improved spatial analysis:
    • NuclearArea (nuclear area in pixels)
    • AreaUm (cellular area in microns)
    • NuclearAreaUm (nuclear area in microns)
    • Xum (X position in microns)
    • Yum (Y position in microns)
  • Expanded the barcodes.parquet** file - Added the following spatial data for each polony:
    • Xum (X position in microns)
    • Yum (Y position in microns)
    • Zum (Z position in microns relative to the Z00 slice)
    • Z (String label of the Z-slice, such as 00 or 01)
  • Added NucleatedRate (percent of cells with a nucleus) to the RunStats.json file
  • New visualization pre-processing outputs - The following files are generated to support future CytoCanvas well visualization:
    • WellInformation.json
    • TileInformation.json
  • Improved segmentation boundary smoothing algorithm - Enhancements retain small cells, small nuclei, and intricate features of neuronal cells, such as axons.

v1.1.0​

February 13, 2025

Improvements​

  • Added target count per area metric to the run statistics file content.
  • Added the --verbose-transfer command, which prints file names to the terminal when logs are copied

v1.0.0​

December 4, 2024

This is the initial release of Cells2Stats. Cells2Stats processes Teton™ Cytoprofiling data to generate detailed statistics and outputs that enable downstream analysis, including visualization using the CytoCanvas tool. 

New Features​

  • Performs target to cell assignment (including RNA and protein targets) and generation of associated raw and normalized metrics files
  • Performs morphology feature extraction from projection images with CellProfiler
  • Prepares run outputs for visualization in CytoCanvas
  • 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.
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