Commands Overview

Pipeline commands are the building blocks of an analysis. Each command takes either an image or a set of objects as input and produces either a processed image or an updated set of objects as output.

Command Categories

Category	Colour	Input	Output
Image processing	Grey	Image	Image
Edge & feature detection	Grey	Image	Image
Segmentation	White	Image	Binary mask
Morphology	White	Binary/greyscale image	Image
AI segmentation	White	Image	Binary mask / object instances
Object processing	Green	Objects	Objects / measurements

Note

Not every command sequence is valid. The command picker shows only those commands compatible with the current pipeline state.

Image Processing

Commands for reducing noise and enhancing signal before segmentation.

Command	Purpose
Blur	Box/average blur to reduce noise
Gaussian Blur	Edge-preserving Gaussian blur
Rolling Ball	Background subtraction
Rank Filter	Min / median / max neighbourhood filter
Enhance Contrast	Histogram-based contrast enhancement
Color Filter	Retain pixels within an HSV colour range
Intensity Transform	Brightness and contrast adjustment
Median Subtract	Subtract the local median for background removal
Image Math	Combine two images mathematically
Image Cache	Store or retrieve an image from cache slots

Edge & Feature Detection

Commands for detecting edges, ridges, and local structures.

Command	Purpose
Canny Edge Detection	Gradient-based edge detection with thresholding
Sobel Edge Detection	Fast gradient-magnitude edge detection
Hessian	Second-order structure (blobs and ridges)
Laplacian	Zero-crossing edge detection
Structure Tensor	Local orientation and coherence
Weighted Deviation	Weighted local standard deviation

Segmentation

Commands for separating foreground objects from background.

Command	Purpose
Threshold	Convert greyscale to binary with manual or automatic threshold
Connected Components	Label each connected foreground region
Watershed	Split touching objects using intensity valleys

Morphology

Commands for modifying the shape of binary or greyscale regions.

Command	Purpose
Morphological Transform	Erosion, dilation, opening, closing

AI Segmentation

Commands that run a pretrained deep-learning model for segmentation. Only available in builds with the ai Cargo feature enabled.

Command	Purpose
Stardist	Instance segmentation via star-convex polygons - separates touching objects directly
UNet	Semantic foreground/background mask - pair with Connected Components (+ Watershed) to separate instances
Cellpose	Instance segmentation via flow-field dynamics - handles irregular and overlapping shapes

Object Processing

Commands that operate on extracted objects.

Command	Purpose
Extract ROIs	Convert binary mask regions to segmentation-class objects
Classify ROIs	Filter and assign final object classes
Colocalization	Find overlapping objects across classes
Voronoi	Partition space from object centroids
Object Transform	Scale, snap, expand, shrink, or fit an ellipse to objects
ROI Math	Boolean set operations (AND, OR, XOR, Subtract) between two object classes
Distance Transform	Measure distances between object pairs
Save Image	Write a control image to disk

Typical Pipeline Order

Image
  └─ Preprocessing (Blur, Rolling Ball, …)
       └─ Segmentation (Threshold → Connected Components → Watershed)
            └─ Extract ROIs
                 └─ Classify ROIs
                      └─ Object Processing (Colocalization, Distance, …)
                           └─ Save Image