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BOM Operation

Removal operations

Six operations that sift a detection by criterion

Definition
Removal operations return the coded imageLoading... they receive, minus some events. Remove labels (larger / smaller) test area in pixels. Remove labels (stronger / weaker) test mean intensity, averaged from a gray image under each event. Remove objects (with seeds) and Remove objects (without seeds) test whether a seed image touches each object. Survivors keep their IDs, so follow with Re-Label (missing)Loading... when numbering matters.
Supporting
Detection - Nuclei Segmentation Classic
Video · Supporting
Detection - Automatic Background Threshold params
Video · Supporting
Pre processing - Import - Coded Image
Video · Supporting
Filter by measured properties
Area and mean intensity are the criteria
Seeds link two detections
Keep events that contain seeds, or that don't
Their place in the workflow
Inside the BOM, not the layer's Post-Processing
Compose multiple criteria with chains
Cascade removals to express AND

Choosing the criterion, by what should survive

Pick the operation by the property that separates the events you want from the rest. Each is named for what it removes, so read the name as its opposite: Remove labels (smaller) keeps the larger events.

Surviving events should be at least a certain size: Remove labels (smaller), with Area threshold (px).

Surviving events should be no larger than a certain size: Remove labels (larger).

Surviving events should be at least a certain brightness: Remove labels (weaker), with Intensity threshold and a gray image as Image 2.

Surviving events should be no brighter than a certain level: Remove labels (stronger).

Surviving events should overlap a known feature mask: Remove objects (without seeds), with the feature mask as Image 2 (seeds). ("Drop events that don't contain a seed" means "keep events that do.") One shared pixel is enough to count as a seed.

Surviving events should NOT overlap a known feature mask: Remove objects (with seeds).

Compound criteria become chains. "Cells larger than N pixels and brighter than X and overlapping the tumor mask" is three operations in sequence, one per criterion. Area is in pixels, so convert a µm² target with the sample area per pixelLoading... first.

Two criteria aren't in this group. Edge contact is handled by Remove objects touching border, and a range on any other measurement by Remove objects v2. Both are engines in the layer's Post-Processing section; see Remove ObjectsLoading....

In image analysis generally, keeping whole objects instead of trimming pixels leaves every survivor exactly as detected, so its area and intensity are unchanged. Keeping the objects a marker touches is what mathematical morphology calls reconstruction from markers; the seeded pair are that idea in one step. Survivors keep their original labels, and the reference names Remove labels as a source of missing labels, so run Re-Label (missing)Loading... afterward if anything downstream requires consecutive numbers.

Source: StrataQuest 8.1 Engines Reference, ch. 6.9 (pp. 284–303); ch. 6.6 (p. 198); ch. 37–38 (pp. 504–507).

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