Some of the most important questions in cell biology aren't about cells, but what's inside them. How many mitochondria per cell? How many DNA damage foci per nucleus? How many lobes in a neutrophil nucleus? The biology varies, the analytical problem is the same: objects within objects, counted and attributed back to their parent.

The challenge is hierarchical. Traditional workflows handle one level of segmentation cleanly. Two levels, with effort. Three levels with intact parent-child relationships, that's where most tools hit their ceiling. Researchers either simplify the question or spend days in custom scripts reconnecting what the analysis disconnected.

Cytely handles the hierarchy natively. Segment cells from one channel, sub-structures from another. The parent-child relationships are automatic. Every object carries its lineage. Number of children, total area of children, mean intensity of children become standard measurements, available for gating and plotting like any other feature.

The result is single-cell resolution on questions that matter. Not "what's the average foci count across the well" but "show me the distribution of foci per cell, and let me gate on the high responders." That's the difference between population blur and biological insight.

How the assay runs

Segment parent objects (e.g., cells) → detect sub-objects within each parent → measure sub-object count, area, intensity, and circularity per parent.

What you provide

  • Ch1: DAPI
  • Ch2: parent object channel (e.g., cell body stain)
  • Ch3: sub-object channel (e.g., organelle marker)

What you get

  • Sub-object count per parent
  • Total sub-object area per parent
  • Mean sub-object intensity
  • Sub-object size distribution

Ready to run

Organelles per cell (mitochondrial fragments, lysosomes, endosomes), inclusions per nucleus (nuclear speckles, Cajal bodies), vesicles per compartment (secretory vesicles, endocytic vesicles), dual sub-object sets per parent (e.g., two organelle types with count ratios).

Inquire for support

Sub-object tracking over time, sub-object-to-sub-object spatial relationships within a parent.

Explore the Sub-Object Quantification assay →