KIC Spheroid Calcium Pipeline — Script 01/03

GUI-based R pipeline for preprocessing, reconstructing, and summarizing calcium transient data from 3D cardiac spheroids generated using the CyteSeer Cytometer (Vala Sciences).

What's included

• GUI selection of input/output paths
• Recursive scanning of CyteSeerResults folders
• Loading of CyteSeer CSV exports (cell-level and whole-image tables)
• Reconstruction of calcium waveform time series from KIC strings
• Computation of additional upstroke and downstroke kinetic parameters
• Export of structured cell-level and whole-spheroid summary datasets

Inputs

• CyteSeerResults export folders
• Primary_DataTable_CStats.csv
• _Cell Peak Measurements_DataTable.csv
• _Whole Image Measurements_DataTable_CStats.csv
• _Whole-Image Peak Measurements_DataTable.csv

(All files must be generated using the Cardiac_Two-Channel_TimeSeries_Extended algorithm in CyteSeer)

Outputs

• Reconstructed calcium waveform datasets
• Derived kinetic parameter tables
• Cell-level summary tables
• Whole-spheroid summary statistics
• Cleaned, standardized outputs ready for downstream analysis

Citation

Developed by Michele Buono, Talitha Spanjersberg, Nikki Scheen, and Nina van der Wilt.
Free for research use and adaptation with citation via Zenodo.