TABLE I.
Comparison of features extracted from chemically stained and virtually stained images for the whole validation dataset (60× magnification). Average and standard deviation of various metrics (pixel value, count, mean area, integrated intensity, mean intensity, and standard deviation of the mean intensity of lipid droplets, cytoplasmic regions, and nuclei) calculated over the 15 sets of target chemically stained images and of the predicted virtually stained images of the validation dataset. We also report the absolute and normalized values of the mean absolute error (MAE and nMAE) as well as the correlation between the metrics calculated on the target and predicted images. Note that the pixel values are in the original image range [0, 65 535], while the intensity measurements are extracted with CellProfiler using images with intensities rescaled from 0 to 1. The features that are most biologically relevant for each cell structure are highlighted (in green, red, and blue for lipid droplets, cytoplasm, and nuclei, respectively).
| Metrics | Target | Prediction | MAE | nMAE (%) | ρ |
|---|---|---|---|---|---|
| Lipid droplets | |||||
| Pixel-value | 1300 ± 180 | 1300 ± 150 | 150 ± 36 | 12 ± 1.3 | 0.98 |
| Count | 6600 ± 580 | 5000 ± 260 | 1600 ± 390 | 24 ± 3.9 | 0.84 |
| Mean area | 400 ± 41 | 550 ± 36 | 160 ± 26 | 41 ± 9.8 | 0.75 |
| Integrated intensity | 13 ± 1.7 | 17 ± 1.7 | 4.2 ± 1.2 | 34 ± 12 | 0.74 |
| Mean intensity | 0.025 ± 0.0027 | 0.023 ± 0.0018 | 0.0016 ± 0.0013 | 6.0 ± 4.2 | 0.80 |
| Std intensity | 0.0035 ± 0.00034 | 0.0037 ± 0.00029 | 0.00027 ± 0.00016 | 8.1 ± 5.4 | 0.76 |
| Cytoplasm | |||||
| Pixel-value | 320 ± 9.9 | 330 ± 7.7 | 59 ± 2.8 | 18 ± 1.0 | 0.77 |
| Count | 34 ± 5.8 | 33 ± 4.0 | 3.1 ± 2.3 | 9.7 ± 7.0 | 0.75 |
| Mean area | 79000 ± 10000 | 82000 ± 11000 | 5800 ± 5000 | 7.3 ± 6.3 | 0.77 |
| Integrated intensity | 430 ± 53 | 460 ± 61 | 41 ± 28 | 9.3 ± 6.1 | 0.74 |
| Mean intensity | 0.0055 ± 0.00015 | 0.0056 ± 0.00013 | 0.00013 ± 0.000085 | 2.5 ± 1.6 | 0.59 |
| Std intensity | 0.0016 ± 0.000083 | 0.0014 ± 0.000034 | 0.00025 ± 0.000073 | 15 ± 3.9 | 0.48 |
| Nuclei | |||||
| Pixel-value | 290 ± 18 | 300 ± 16 | 92 ± 7.6 | 32 ± 2.5 | 0.82 |
| Count | 34 ± 5.8 | 33 ± 4.0 | 3.1 ± 2.1 | 9.7 ± 7.0 | 0.75 |
| Mean area | 7400 ± 1100 | 7100 ± 1100 | 320 ± 240 | 4.2 ± 3.1 | 0.93 |
| Integrated intensity | 170 ± 24 | 170 ± 26 | 9.4 ± 5.6 | 5.6 ± 3.4 | 0.90 |
| Mean intensity | 0.022 ± 0.00081 | 0.022 ± 0.00084 | 0.00068 ± 0.00060 | 3.1 ± 2.8 | 0.37 |
| Std intensity | 0.0065 ± 0.00042 | 0.0054 ± 0.00026 | 0.0011 ± 0.00043 | 16 ± 6.0 | 0.28 |