Table 2.
Performance of the proposed de-arraying method on three datasets under four setting options: (1) both the segmentation and the non-linear estimation (for the deformation) modules are deactivated, (2) the segmentation is activated but the non-linear estimation is deactivated, (3) the segmentation is deactivated and the non-linear estimation is activated, and (4) both of them are activated
| Localization | Estimation of array coordinates | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A (a) | P (b) | R (c) | F (d) | G (e) | JSC (f) | A (a) | P (b) | R (c) | F (d) | G (e) | JSC (f) | |
| SIMULATED IMAGES | ||||||||||||
| Average on 31 images | ||||||||||||
| Wang et al. [22] | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| ATMAD Opt. #1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.93 | 1 | 0.93 | 0.96 | 0.96 | 0.93 |
| Opt. #2 | 0.95 | 1 | 0.95 | 0.98 | 0.98 | 0.95 | 0.85 | 1 | 0.84 | 0.91 | 0.91 | 0.84 |
| Opt. #3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #4 | 0.95 | 1 | 0.95 | 0.98 | 0.98 | 0.95 | 0.95 | 1 | 0.95 | 0.98 | 0.98 | 0.95 |
| Fig. 11a | ||||||||||||
| ATMAD Opt. #1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #2 | 0.97 | 1 | 0.96 | 0.98 | 0.98 | 0.96 | 0.97 | 1 | 0.96 | 0.98 | 0.98 | 0.96 |
| Opt. #3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #4 | 0.97 | 1 | 0.96 | 0.98 | 0.98 | 0.96 | 0.97 | 1 | 0.96 | 0.98 | 0.98 | 0.96 |
| Fig. 11b | ||||||||||||
| ATMAD Opt. #1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.93 | 1 | 0.92 | 0.96 | 0.96 | 0.92 |
| Opt. #2 | 0.93 | 1 | 0.92 | 0.96 | 0.96 | 0.92 | 0.90 | 1 | 0.89 | 0.94 | 0.95 | 0.89 |
| Opt. #3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #4 | 0.93 | 1 | 0.92 | 0.96 | 0.96 | 0.92 | 0.93 | 1 | 0.92 | 0.96 | 0.96 | 0.92 |
| BRIGHTFIELD IMAGES | ||||||||||||
| Average on 8 images | ||||||||||||
| ATMAD Opt. #1 | 0.94 | 1 | 0.93 | 0.96 | 0.96 | 0.93 | 0.91 | 1 | 0.88 | 0.94 | 0.94 | 0.88 |
| Opt. #2 | 0.87 | 1 | 0.83 | 0.91 | 0.91 | 0.83 | 0.84 | 1 | 0.79 | 0.88 | 0.89 | 0.79 |
| Opt. #3 | 0.94 | 1 | 0.93 | 0.96 | 0.96 | 0.93 | 0.94 | 1 | 0.93 | 0.96 | 0.96 | 0.93 |
| Opt. #4 | 0.87 | 1 | 0.83 | 0.91 | 0.91 | 0.83 | 0.93 | 1 | 0.91 | 0.95 | 0.95 | 0.91 |
| Fig. 12 | ||||||||||||
| ATMAD Opt. #1 | 0.96 | 1 | 0.94 | 0.97 | 0.97 | 0.94 | 0.91 | 1 | 0.89 | 0.94 | 0.94 | 0.89 |
| Opt. #2 | 0.87 | 1 | 0.83 | 0.91 | 0.91 | 0.83 | 0.84 | 1 | 0.80 | 0.89 | 0.89 | 0.80 |
| Opt. #3 | 0.96 | 1 | 0.94 | 0.97 | 0.97 | 0.94 | 0.96 | 1 | 0.94 | 0.97 | 0.97 | 0.94 |
| Opt. #4 | 0.87 | 1 | 0.83 | 0.91 | 0.91 | 0.83 | 0.93 | 1 | 0.91 | 0.95 | 0.95 | 0.91 |
| FLUORESCENCE IMAGES | ||||||||||||
| Average on 8 DNA microarray images | ||||||||||||
| ATMAD Opt. #1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #4 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Fig. 13 | ||||||||||||
| ATMAD Opt. #1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Opt. #4 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Average on 4 TMA images | ||||||||||||
| ATMAD Opt. #1 | 0.79 | 0.77 | 1 | 0.87 | 0.88 | 0.77 | 0.92 | 0.98 | 0.93 | 0.95 | 0.95 | 0.91 |
| Opt. #2 | 0.91 | 0.99 | 0.90 | 0.94 | 0.95 | 0.89 | 0.73 | 1 | 0.69 | 0.82 | 0.83 | 0.69 |
| Opt. #3 | 0.79 | 0.77 | 1 | 0.87 | 0.88 | 0.77 | - | - | - | - | - | - |
| Opt. #4 | 0.91 | 0.99 | 0.90 | 0.94 | 0.95 | 0.89 | 0.92 | 0.98 | 0.93 | 0.96 | 0.96 | 0.91 |
| Fig. 14 | ||||||||||||
| ATMAD Opt. #1 | 0.88 | 0.86 | 1 | 0.93 | 0.93 | 0.86 | 0.94 | 1 | 0.94 | 0.97 | 0.97 | 0.94 |
| Opt. #2 | 0.86 | 1 | 0.84 | 0.91 | 0.92 | 0.84 | 0.80 | 1 | 0.77 | 0.87 | 0.88 | 0.77 |
| Opt. #3 | 0.88 | 0.86 | 1 | 0.93 | 0.93 | 0.86 | 0.97 | 1 | 0.97 | 0.98 | 0.98 | 0.97 |
| Opt. #4 | 0.86 | 1 | 0.84 | 0.91 | 0.92 | 0.84 | 1 | 1 | 1 | 1 | 1 | 1 |
All considered performance scores range from 0 (worst) to 1 (best) and measure the similarity between the de-arraying results and their corresponding ground-truth or manual annotation. Notations: (a) accuracy (A), (b) precision (P), (c) recall (R), (d) F-score (F), (e) G-score (G) and (f) Jaccard coefficient (JSC)