Cells2Stats Release Notes

v1.2.0

April 8, 2025

Improvements

• Enhanced the RawCellStats file - Added the following fields for improved spatial analysis:
  • NuclearArea (nuclear area in pixels)
  • Area μm (cellular area in microns)
  • NuclearAreaUm (nuclear area in microns)
  • X μm (X position in microns)
  • Y μm (Y position in microns)
• Expanded the barcodes.parquet file - Added the following spatial data for each polony:
  • X μm (X position in microns)
  • Y μm (Y position in microns)
  • Z μm (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.