Table 3 Summarised network performance for the different tasks and datasets.
From: DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches
Task | Organism | Dataset | Figure | Network | Network performance | |||||
|---|---|---|---|---|---|---|---|---|---|---|
IoU | Precision | Recall | mAP | SSIM | PSNR | |||||
Segmentation | S. aureus | Bright field | 2B | StarDist | 0.64 ± 0.01 | 0.90 ± 0.03 | 0.87 ± 0.03 | – | – | – |
S. aureus | fluorescence | 2B | StarDist | 0.91 ± 0.03 | 0.98 ± 0.02 | 1.00 ± 0.01 | – | – | – | |
E. coli | Bright field | 2C | U-Net | 0.82 ± 0.03 | 0.56 ± 0.20 | 0.39 ± 0.20 | – | – | – | |
E. coli | Bright field | 2C | ML-U-Net | 0.78 ± 0.05 | 0.71 ± 0.11 | 0.81 ± 0.09 | – | – | – | |
E. coli | Bright field | 2C | CARE | 0.83 ± 0.03 | 0.85 ± 0.06 | 0.78 ± 0.09 | – | – | – | |
E. coli | Bright field | 2C | StarDist | 0.78 ± 0.03 | 0.83 ± 0.12 | 0.87 ± 0.07 | – | – | – | |
E. coli | Bright field | 2C | pix2pix | 0.86 ± 0.02 | 0.82 ± 0.07 | 0.64 ± 0.12 | – | – | – | |
B. subtilis | fluorescence | 2D | U-Net | 0.78 ± 0.06 | 0.67 ± 0.21 | 0.63 ± 0.26 | – | – | – | |
B. subtilis | fluorescence | 2D | ML-U-Net | 0.82 ± 0.02 | 0.79 ± 0.16 | 0.82 ± 0.20 | – | – | – | |
B. subtilis | fluorescence | 2D | CARE | 0.74 ± 0.04 | 0.44 ± 0.28 | 0.36 ± 0.23 | – | – | – | |
B. subtilis | fluorescence | 2D | StarDist | 0.76 ± 0.03 | 0.88 ± 0.05 | 0.92 ± 0.05 | – | – | – | |
B. subtilis | fluorescence | 2D | SplineDist | 0.72 ± 0.04 | 0.88 ± 0.06 | 0.87 ± 0.10 | – | – | – | |
B. subtilis | fluorescence | 2D | pix2pix | 0.69 ± 0.07 | 0.69 ± 0.20 | 0.64 ± 0.21 | – | – | – | |
all above | mixed model | S2 | StarDist | 0.74 ± 0.06 | 0.88 ± 0.08 | 0.84 ± 0.14 | – | – | – | |
E. coli | Bright field (stat. Phase) | 2E | StarDist | 0.83 ± 0.02 | 0.95 ± 0.04 | 0.97 ± 0.03 | – | – | – | |
Object detection | E. coli | Growth stage (large FoV) | – | YOLOv2 | – | 0.65 ± 0.10 | 0.47 ± 0.09 | 0.39 ± 0.09 | – | – |
E. coli | Growth stage (small FoV) | 3A | YOLOv2 | – | 0.73 ± 0.03 | 0.74 ± 0.08 | 0.67 ± 0.10 | – | – | |
E. coli | Antibiotic profiling | 3B | YOLOv2 | – | 0.76 ± 0.13 | 0.76 ± 0.23 | 0.66 ± 0.23 | – | – | |
Denoising | E. coli | H-NS-mScarlet-I | 4A | PureDenoise | – | – | – | – | 0.834 ± 0.013 | 33.5 ± 0.9 |
E. coli | H-NS-mScarlet-I | 4A | Noise2Void | – | – | – | – | 0.881 ± 0.005 | 34.9 ± 0.9 | |
E. coli | H-NS-mScarlet-I | 4A | CARE | – | – | – | – | 0.897 ± 0.005 | 36.1 ± 0.9 | |
E. coli | MreB-sfGFP | 4E | PureDenoise | – | – | – | – | 0.458 ± 0.013 | 26.2 ± 0.9 | |
E. coli | MreB-sfGFP | 4E | CARE | – | – | – | – | 0.520 ± 0.010 | 27.0 ± 0.8 | |
B. subtilis | FtsZ | 4G | Noise2Void | – | – | – | – | - | - | |
Artificial labelling | E. coli | Widefield | 5A | CARE | – | – | – | – | 0.83 ± 0.05 | 24.4 ± 1.2 |
E. coli | Widefield | 5A | fnet | – | – | – | – | 0.88 ± 0.06 | 25.9 ± 1.7 | |
E. coli | PAINT | 5A + S8 | CARE | – | – | – | – | 0.85 ± 0.05 | 24.0 ± 1.2 | |
E. coli | PAINT | 5A + S8 | fnet | – | – | – | – | 0.85 ± 0.07 | 24.3 ± 1.4 | |
Resolution enhancement | E. coli | WF/SIM | 6A | CARE | – | – | – | – | 0.84 ± 0.03 | 25.4 ± 1.0 |
S. aureus | WF/SIM | 6B | CARE | – | – | – | – | 0.92 ± 0.01 | 28.2 ± 0.7 | |
