## 3 Experiment
### Virus Detection Algorithm
Figure 9: Box plots comparing the algorithm performance to expert counts. (**a**) Box plot for the cell counting algorithm, and (**b**) box plot for the virus counting algorithm, assessing whether the algorithms fall within the range of expert counts. To evaluate how well the algorithm performs in comparison to expert counts, the percentage of algorithm-generated cell counts that fall within these ranges was calculated. The results indicate that 90.13% of the algorithm's data fall within the whiskers, demonstrating that the algorithm's output is generally in line with expert assessments, with only a small proportion of outliers. Additionally, 82.24% of the algorithm's data lie within the IQR, which highlights that most of the algorithm's results are consistent with the central tendency of the expert counts. This suggests that the algorithm performs with a high degree of accuracy and consistency, as its results largely overlap with the expert-derived quartiles. The box plot for the virus detection algorithm, shown in Figure 9b, highlights the distribution of virus counts based on expert assessments, with a focus on evaluating how the algorithm's results align with the experts' counts. In this analysis, 86.67% of the algorithm's data fall within the whiskers, indicating a high degree of consistency with the experts' results. Additionally, 68.0% of the algorithm's data are within the interquartile range (IQR), suggesting a slightly wider spread compared to the cell counting algorithm. Despite the broader range within the IQR, the algorithm's performance remains robust, with most data points aligning closely with expert evaluation. ## 5 Discussion

After validating the performance of the cell and virus detection algorithms, these tools were applied in a laboratory setting to evaluate how different inhibitors affect the Chikungunya virus. In the experimental setup, as shown in the image in Figure 10, several inhibitors were tested across multiple wells, along with key control groups: cell + viruses (positive control), cell + DMSO, and cells (negative control). For each well, the cell detection algorithm was used to count the number of cells, and the virus detection algorithm quantified the number of viral particles. The positive control, cell + viruses, served as a reference for maximum viral presence, while the negative control, cells, indicated the baseline where no virus was present, confirming normal cell growth. The cell + DMSO wells were included to account for any potential effects of the solvent (DMSO) used to dissolve the inhibitors. Each inhibitor was tested in duplicate wells to ensure accurate measurements, and the cell and virus counts from each well were averaged to improve reliability. The averaged data were then used to calculate the percentage of cell viability, which reflects how well the cells survive in the presence of the inhibitor. The percentage of viral inhibition measures the inhibitor's effectiveness in reducing viral presence compared to the positive control. Figure 10: Merged fluorescence images of cells infected with the chikungunya virus (CHIKV) at an MOI of 0.5, incubated for 1 day. Rows (A–D) and columns (1–12) represent different sample wells, with specific conditions or treatments labeled above the wells. The results from these calculations are plotted to show the percentage of viral inhibition and cell viability for each inhibitor. The controls play an essential role in interpreting these results. The cell + viruses control represents the maximum viral activity, serving as a baseline for comparing inhibitor effectiveness. The cell + DMSO control ensures that any reduction in viral counts is due to the inhibitor and not the solvent, while the cell control shows the normal cell count in the absence of the virus, confirming the health of the cell culture. This approach enables the identification of inhibitors that effectively reduce viral counts without significantly impacting cell viability, which is crucial for selecting candidates for further experimentation.