Image Standardization
Flatfield correction, background subtraction, illumination normalization. Removes spatial and intensity bias at the acquisition level before any downstream quantification.
Module details
Platform
The Cytely Analysis Engine
A standardization layer that integrates before your existing image analysis pipeline — delivering reproducible quantitative outputs across instruments, sites, and time points.
Architecture
Standardization pipeline
The Analysis Engine processes images in a sequential, auditable pipeline. Each stage can be configured and saved as a protocol for your specific instrument setup.
Modules
Three modules. One pipeline.
Cytely's modular architecture lets you apply exactly the correction steps relevant to your workflow.
Quantification
Cell and object segmentation, feature extraction, biomarker intensity quantification. Outputs structured per-object data tables compatible with CellProfiler, MATLAB, and Python.
Module detailsBatch Analysis
High-throughput plate-reader and HCS-compatible batch processing. Handles 96-well, 384-well, and custom plate formats with per-well quality control reporting.
Module detailsTechnical Specifications
System requirements and compatibility
| Category | Specification | Notes |
|---|---|---|
| Operating system | Windows 10/11 (64-bit), macOS 12+, Ubuntu 20.04+ | Linux requires glibc 2.31+ |
| RAM (recommended) | 16 GB minimum; 32 GB for batch HCS workflows | Large z-stack sets benefit from 64 GB+ |
| File formats (input) | TIFF, CZI, LIF, ND2, IMS, VSI, OIB, OME-TIFF |
Via Bio-Formats reader integration |
| Output formats | OME-TIFF, TIFF, CSV, HDF5 |
Per-image, per-well, per-plate summaries |
| API interface | Python SDK (pip), MATLAB toolbox, REST API (Lab license+) | Python 3.9+; MATLAB R2022a+ |
| Plugin interfaces | FIJI/ImageJ plugin, CellProfiler module | Available in Lab and Commercial tiers |
| License delivery | License key via email; node-locked or floating (Commercial) | Annual renewal; offline activation available |
| Validation documentation | IQ/OQ/PQ support package (Commercial tier) | GxP-ready audit trail available as add-on |
Reproducibility
Before and after standardization
Intensity coefficient of variation (CV%) across three confocal systems measuring the same DAPI-stained slide, with and without Cytely standardization. Residual CV after correction reflects biological heterogeneity within the sample, not instrument variability.
Inter-instrument intensity CV% — DAPI channel
Without Cytely
With Cytely
Representative data from internal validation studies. Results vary by sample type and imaging conditions.
Discuss your imaging setup
Our application scientists can advise on the appropriate correction strategy for your instrument configuration — confocal, widefield, HCS platform, or mixed fleet.