Table 2. Spot detection algorithms tested.
| Method | Type/origin | Parameters | Source | |
|---|---|---|---|---|
| Houghpeaks (HP) | designed for identifying peaks in images | Intensity threshold Ithresh | 11–25 pc (450–800) pc |
Matlab image processing toolbox |
| Vertical and horizontal spot size NhoodSizea | 1, 3, 5, 7, 9 pixels |
|||
| max. number of spots | 9000 | |||
| in-series screening (ISS) | home-built algorithm inspired from HP | see HP | MASH-FRET | |
| Schmied (SCH) | designed for super-resolution microscopy | min. intensity-to-background ratio | 1.5–3 a.u. (1.05–3) |
[66] |
| min. distance to image edge | 3 | |||
| TwoTone (2tone) | designed for analyzing smFRET SMVs | Intensity threshold Ithresh | 1–6 a.u. | [15] |
| bandpass filter kernel BpSize | (4–6) a.u. 1, 3, 5, 7, 9 |
|||
Input parameters in brackets are specific to the analysis of time-averaged SMVs.
a”The suppression neighborhood is the neighborhood around each peak that is set to zero after the peak is identified.” Compare Matlab documentation.