Contains the program "iSort" to automate and monitor high-throughput droplet screening. The program is linked to the following publication: iSort enables automated complex microfluidic droplet sorting in an effort to democratize technology. Abstract: Fluorescence activated droplet sorting (FADS) is a widely used microfluidic technique for high throughput screening. However, it requires highly trained specialists to determine optimal sorting parameters, resulting in a large combinatorial space that is challenging to optimize systematically. Additionally, there is currently no way to track every single droplet within a screen, leading to compromised sorting and “hidden” false positive events. To overcome all these limitations, we have developed a setup in which the droplet frequency, spacing and trajectory at the sorting junction are monitored in real time using impedance analysis. The resulting data is used to continuously optimize all parameters automatically and to counteract perturbations, resulting in higher throughput, higher reproducibility, increased robustness and a beginner-friendly character. We believe this provides a missing piece for the spreading of phenotypic single-cell analysis methods, similar to what we have seen for single-cell genomics platforms. To cite: https://doi.org/10.1016/j.crmeth.2023.100478