Classify ROIs

The Classify ROIs command takes segmentation-class objects produced by Extract ROIs and applies a set of shape and intensity filters. Objects that pass all filters are assigned to the target class; objects that fail are discarded.

This is where raw segmentation output (“every connected group of bright pixels”) turns into biological meaning (“this is a nucleus, that speck isn’t”) - the filters exist because segmentation almost always over-detects, picking up noise, debris, and imaging artifacts alongside genuine objects.

Input Selection

Parameter	Description
Origin segmentation	One or more segmentation classes to process
Origin class	Alternatively, input already-classified objects from named classes

Target Class

Parameter	Description
Target class	The named object class assigned to objects that pass all filters

Shape Filters

All shape-based filters accept –1 as “no limit” for the upper bound and 0 / –1 for “no lower limit”.

Filter	Description
Min area / Max area	Object area in px² (or µm² depending on Size unit)
Min circularity / Max circularity	Range 0.0–1.0; 1.0 = perfect circle
Min solidity / Max solidity	Ratio of area to convex hull area (0–1)
Min aspect ratio / Max aspect ratio	Bounding box width / height ratio
Min eccentricity / Max eccentricity	Elongation from fitted ellipse (0 = circle, 1 = line segment)
Min Feret / Max Feret	Maximum calliper (Feret) diameter
Allow edge touching	If disabled, objects that touch the image border are discarded

Size unit

Shape filters that depend on physical size (area, Feret) can use:

• Pixels (px) - absolute pixel count
• Micrometres (µm) - converted using the pixel size from image metadata

Intensity Filters

Filter	Description
Min mean intensity / Max mean intensity	Average pixel intensity within the object
Intensity unit	Absolute (0–65535), Percent (0–100), or Relative (0–1)

Intensity is measured in the channel/plane configured in the input address. Set –1 to disable either bound.

Example: Spot detection

Min area:        3 px²
Max area:        -1 (no upper limit)
Min circularity: 0.1
Max circularity: -1
Allow edge touching: true

This retains objects larger than 3 pixels with any shape, discarding single-pixel noise.