Abstract. Post-acquisition data analysis of microscopy images is a vital yet time-consuming process for researchers. Quantitative fields such as biology and microbiology often require using images as primary data sources. Finding methods to automate this process would increase the throughput, quality, and reproducibility. This research aims to provide a novel end-to-end pipeline that reduces the workload on researchers in identifying cell cytoplasm and nuclei while creating a process that can scale to the researcher\u27s needs. The proposed methodology utilizes various image-processing techniques to rapidly identify the boundaries of cells and nuclei, including filtering, thresholding, and deep learning. The results of this research indicate that the proposed methodology could be a valuable tool for microbiologists, saving time and effort for accurate data collection
