Table 1.
Summary of existing cell segmentation and FRET quantification software
| Software | Description | ROI | Cell Segmentation | FRET/Intensity Quantification | Reference |
|---|---|---|---|---|---|
| FRETzel | Cell segmentation through circular active contouring, including cell and ROI intensity quantification | Yes | Yes | yes | This study |
| CellX | Cell segmentation using membrane patterns, includes some intensity quantification | No | failed on adipocytes | yes | (Mayer et al., 2013) |
| CellProfiler | Open platform for cell image analysis, which supports manual segmentation and intensity quantification through pipeline development | Yes | yes - but only by manual drawing of cell boundaries | yes | (McQuin et al., 2018) |
| CellSegm | Membrane stain based cell segmentation | No | requires membrane staining | no | (Hodneland et al., 2013) |
| OMAL Toolbox | MATLAB toolbox for cell image analysis | No | requires fluorescence | no | (Baggett et al., 2005) |
| AccPbFRET | FRET quantification toolbox | Yes | No | yes | (Roszik et al., 2008) |
| FLIM-FRET analyzer | FRET quantification toolbox with fluorescence based cell segmentation | Yes | requires fluorescence | yes | (Kim et al., 2017) |
This includes whether they support region of interest (ROI) based quantification, cell segmentation, and intensity quantification.