The Cytely quantification module provides reproducible per-object measurements from standardized fluorescence images — cell counts, intensity distributions, morphology features, and co-localization metrics.
Quantification Module
Capabilities
Nucleus and cytoplasm segmentation using watershed, Otsu thresholding, or intensity-based boundary detection. Supports primary object detection (nuclei), secondary object expansion (cytoplasm), and tertiary mask subtraction. Configuration parameters are saved per protocol.
Per-object measurements: mean, median, integrated intensity, area, eccentricity, solidity, Zernike moments, texture (Haralick), and user-defined region-of-interest measurements. Output includes per-channel intensity features for multi-marker panels.
Standardized intensity values enable direct biomarker comparison across experiments and instrument configurations. Cytely outputs per-cell biomarker intensity as normalized fluorescence units — directly usable in downstream statistical analysis without manual adjustment.
Output
Cytely outputs per-object data tables in standard formats compatible with CellProfiler, MATLAB, R, and Python.
| Column | Type | Description |
|---|---|---|
object_id | integer | Unique per-object identifier within image |
image_id | string | Source image filename with acquisition metadata |
well_id | string | Plate well identifier (e.g. A03) |
ch{n}_mean_intensity | float | Mean standardized intensity per channel n |
ch{n}_integrated_intensity | float | Integrated (total) standardized intensity |
area_px | integer | Object area in pixels |
area_um2 | float | Object area in µm² (requires calibrated pixel size) |
eccentricity | float | Shape eccentricity (0=circle, 1=line) |
cytely_protocol_version | string | Protocol identifier used for standardization |
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