The image standardization module corrects systematic sources of intensity variability at the optical and detector level — before any segmentation or measurement runs on your data.
Image Standardization Module
Corrects for non-uniform illumination across the field of view. Cytely estimates the flatfield function from reference images (slide blank, averaged sample images, or empirical background) and applies a per-pixel correction. Intensity at image edges, which is typically 15–25% lower than at center in widefield configurations, is restored to uniformity.
Removes autofluorescence and detector dark-current offset using configurable strategies: rolling-ball background estimation, blank-image reference, or channel-specific offset. Preserves signal-to-noise ratio in dim channels while preventing intensity inflation in bright-field contamination scenarios.
Maps fluorescence intensity distributions from multiple acquisition systems to a common reference frame. Cytely uses fluorescent reference standards or shared sample anchors to derive per-channel gain correction factors — enabling direct comparison of measurements from different ZEISS, Leica, Nikon, or Olympus systems.
Protocol
Each parameter set can be saved as a named protocol tied to a specific instrument configuration. Protocols are versioned and auditable.
| Parameter | Options | Default |
|---|---|---|
flatfield_mode | reference, empirical, blind | empirical |
background_method | rolling_ball, blank_image, offset_constant | rolling_ball |
normalization_reference | Path to reference standard image set | None |
per_channel | true, false | true |
output_bit_depth | 16bit, 32bit_float | 16bit |
clip_negative | true, false | true |
The right flatfield mode depends on whether you have access to a blank slide reference or need to estimate the flatfield empirically. Our application scientists can advise based on your instrument configuration.