Grow

Grow (global) sits in a layer's Measurements Masks section (Add > Operations (basic) > Grow (global)). It takes a set of detected events, a coded imageLoading..., and generates new measurement masks from them. Every mode uses each event's contour as its starting point.

• Grow inflates each event body by the Grow radius.
• Shrink deflates it by the Shrink radius.
• Shrink (retain last pixel) deflates it too, but keeps the last pixel of an event smaller than the radius.
• Ring grows inward by the Interior radius and outward by the Exterior radius, from a contour that Skip distance can shift outward first. Include seeds adds the original body, like an Or of the two masks.

In every mode a Mask input marks, in white, where growing or shrinking is allowed. The result is a coded image of the grown, shrunk or ring-shaped events, which a Measurements engine can take as its coded input in place of the original bodies.

Dilation and erosion, in general. In mathematical morphology, growing an object is called dilation and shrinking it erosion. Take a small disk, the structuring elementLoading..., and roll it along the outside of the object's edge: everything it sweeps joins the object. Rolled along the inside, it carves the object down. The Engines Reference doesn't say how StrataQuest measures the radius, so this is the textbook picture, and the morphological operationsLoading... page covers the family.

What growing can't do. Erosion and dilation aren't inverses. Shrink a small object until it disappears and no amount of growing brings it back, which is what Shrink (retain last pixel) guards against. Growing also can't restore boundary detail lost at detection, so choose radii from the biology you want to capture, not to patch a detection.

When neighbors collide. Grow two nearby nuclei and their grown masks can reach the same pixel. In image processing generally, one common rule gives each contested pixel to the nearest object, which divides the space between nuclei along the midline, much like a Voronoi diagram. StrataQuest's Basic Operations Module documents that rule for its Grow labels operation, where each pixel is assimilated by the closest label. For Grow (global) the Engines Reference doesn't say how a collision is resolved.

Why rings help. A cytoplasmic or membrane marker contributes little inside the nucleus, so its mean over the nuclear area mostly measures whatever happens to overlap it. A ring that starts at the nuclear contour samples the zone around the nucleus instead. Without a membrane stain, the ring's width is a guess about how far the cytoplasm reaches. The MembraneLoading... engine, and the identified mask of the Cellular engine, let a stain set that boundary instead.

The reference example grows and shrinks by 10 µm, so the radii can be set in micrometers. For a first ring, try Interior radius 0 and a small Exterior radius, then compare the overlay with the cells you see.

Source: StrataQuest 8.1 Engines Reference, ch. 24 (pp. 438–443); ch. 6.6 (p. 191); ch. 7 (pp. 361–364); ch. 29 (p. 465); ch. 41 (p. 538).

Suppose you've detected nuclei on DAPI in a multiplex immunofluorescence scan and want a cytoplasmic marker for each cell.

1. Nuclear compartment: the NucleiLoading... events themselves.
2. Inner ring: add Grow (global) in Measurements Masks with Mode Ring, Interior radius 0 and Exterior radius 3 µm, a band hugging the outside of each nucleus.
3. Outer band: a second Grow (global) in Ring mode with Skip distance 3 µm and Exterior radius 6 µm starts where the first ring ends.
4. Measure: add a Standard MeasurementsLoading... engine for each compartment and marker, with the grown events as Coded and the marker channel as Shades.

The radii here are illustrations. Set yours from the cell types in front of you, and check the overlay where cells crowd together. If you need nuclear, ring and stain-identified masks at once, the Cellular engine in the same category makes all three.