The Cytely Batch Analysis module applies the full standardization and quantification pipeline to entire 96-well or 384-well plates in a single run — with per-well quality control reporting and structured data output.
Batch Analysis Module
Capabilities
Processes 96-well, 384-well, and custom plate layouts. Automatically parses plate maps from CSV or Excel, assigns per-well compound identifiers, and organizes outputs by well position. Compatible with all major HCS file structures.
Automated QC flags per well: cell count thresholds, focus score, signal-to-noise ratio, and edge-effect detection. QC summary report generated per plate run with configurable pass/fail thresholds. Flagged wells are excluded from aggregate statistics.
Per-well summary statistics, per-object data tables, and plate-level aggregates. All outputs include Cytely protocol metadata for provenance tracking. Compatible with CellProfiler Analyst, KNIME, R, and Python pandas.
| Parameter | Value |
|---|---|
| Supported plate formats | 96-well, 384-well, 1536-well, custom |
| Max plates per run | Unlimited (Academic); configurable queue depth (Commercial) |
| Parallelisation | Multi-core CPU; GPU acceleration (CUDA) for segmentation (Commercial) |
| Output formats | CSV, HDF5, SQLite, OME-TIFF (standardized images) |
| API trigger | Python SDK, REST endpoint, CLI (Lab+) |
| Audit trail | Full run log with protocol version, hash of input images, processing timestamps |
Contact us to discuss integration with your existing plate-reader infrastructure.