Application Note: Spot & Foci Detection

This isn't one assay. It's the capability that powers half of modern cell biology. γH2AX foci. RNAscope dots. PLA puncta. Stress granules. P-bodies. PML bodies. Pathogen cells. Lipid droplets. Synaptic puncta. Drug aggregates. They are all the same analytical problem: small bright objects inside cells that need to be detected, counted, and measured per cell.

The manual version of this, a researcher squinting at images, clicking on dots, tallying counts in a spreadsheet, is one of the most common time sinks in biological research. A single DNA damage experiment can require counting foci in 200+ nuclei. An RNAscope experiment multiplies that by the number of probe channels.

Cytely's spot detection engine is the shared foundation beneath all of these assays. It detects puncta, measures count, area, and intensity per cell, and feeds those measurements into the same interactive gating and image-linking interface that powers every other Cytely analysis.

How the assay runs

Segment nuclei/cells from DAPI → detect puncta in target channel → count and measure per cell.

What you provide

Ch1: DAPI
Ch2: channel containing punctate structures (IF, FISH probe, or fluorescent tag)

What you get

Spot count per cell
Total spot area per cell
% cells with spots
Per-spot measurements (area
Mean/median/min/max intensity
Integrated (sum) intensity
Circularity
Elongation (major/minor axis ratio), orientation, centroid position)

Ready to run

DNA damage foci (γH2AX, 53BP1, RAD51), RNA puncta (RNAscope, smFISH), stress granules (G3BP1), P-bodies (DCP1A), PML bodies, synaptic puncta, receptor clusters, drug aggregates, viral particles, lipid droplets, any sub-cellular punctate structure.