| Operation | Inputs | Description |
|---|---|---|
| Convert 16→8 bit | 16-bit grayscale | Linear mapping from 16-bit to 8-bit. With range selection: maps user-specified 16-bit [min, max] to [0, 255], clipping values outside the range. |
| Extract channel | Multi-channel/RGB image + channel index | Outputs a single grayscale image corresponding to the specified channel (e.g., R=0, G=1, B=2 for RGB images). |
| Extract strongest channel | Multi-channel image | At each pixel, selects the channel with the highest intensity. Useful for identifying the dominant signal in multi-stain images. |
| Mask | Source image + binary mask | Multiplies source by mask: pixels inside the mask pass through, pixels outside become zero. |
| Set channels to RGB | 3 grayscale images | Assembles three separate grayscale images into a single RGB image by assigning each to the R, G, or B channel. |
| Swap channels | Multi-channel image | Reorders channel assignments (e.g., swap R↔B to convert between RGB and BGR ordering conventions). |
BOM Group
Image Data Operations
Format conversion and channel manipulation utilities
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Definition
Utility operations for image format manipulation — converting bit depth, extracting or swapping channels, applying masks, and assembling RGB composites — providing the plumbing that connects different stages of multi-channel analysis pipelines.
Six Utility Operations
Bit depth, channel extraction, masking, RGB assembly
Bit-Depth Conversion
16-bit → 8-bit with range selection
Channel Manipulation
Extract, swap, and reassemble color channels
Masking
Zero all pixels outside a binary mask region
Operations Reference
Simplified
These are utility tools: Convert 16→8 bit reduces bit depth. Extract channel pulls out a single color channel. Extract strongest finds the brightest channel per pixel. Mask restricts processing to specific areas. Set channels to RGB builds color images from separate channels. Swap channels reorders color assignments.
When to Use Which
Bit-Depth Conversion
Convert 16→8 bit — Use when downstream operations require 8-bit input, or when the useful signal occupies only a small portion of the 16-bit range. Setting range [200, 8000] → [0, 255] optimizes contrast for the signal of interest without losing meaningful data.
Channel Extraction
Extract channel — Use to isolate a specific fluorescence channel or color component for targeted BOM processing. Example: extract the green channel from an RGB brightfield image before applying stain-specific processing.
Extract strongest channel — Use when you need the dominant signal regardless of which channel it comes from. Useful for creating a combined detection input from channels with partially overlapping staining patterns.
Masking and Assembly
Mask — Apply before any operation that should be restricted to a specific tissue region. The mask is typically generated from Tissue Detection or Classifier output.
Set channels to RGB — Assemble pseudo-color composites for visualization, or convert separated stain channels back into a composite RGB view.
Swap channels — Handle images where channel ordering doesn't match expected conventions (e.g., RGB vs. BGR from different scanner platforms).
Simplified
Use Convert 16→8 bit when you need 8-bit data or want to optimize contrast. Use Extract channel to work with a single channel. Use Mask to restrict operations to tissue areas. Use Set channels to RGB to create color composites for review.