Watershed

The Watershed command separates objects that are close together or touching by treating pixel intensities as altitude and finding the valleys between peaks. It is placed after Connected Components.

When to use

Use Watershed when high object density causes nearby objects to be detected as a single merged region after thresholding. Typical scenarios:

• Dense vesicle populations
• Touching cell nuclei

Performance

Watershed is a computationally expensive algorithm. Enable it only when necessary, as it significantly increases analysis time.

Parameters

Parameter	Description
Maximum finder tolerance	Controls sensitivity to local intensity peaks. Range: 0.0–1.0. Lower values detect more (smaller) peaks and split more aggressively; higher values require more prominent peaks.

How it works

1. The distance-transform of the binary mask is computed.
2. Local maxima in the distance map are found using the tolerance parameter.
3. Each maximum is treated as a “seed” and the mask is flooded outward from each seed simultaneously.
4. Where the flooding fronts from different seeds meet, a watershed line is drawn.

The implementation is ported from ImageJ.