My role was developing software and image processing pipelines for analyzing 3D microscopy data. In particular, I specialized in quantifying cell movements in 3D and segmenting movement patterns of tissues. For this, I developed one of the fastest open-source PIV packages (quickPIV) in Julia. Optimizing PIV required delving to low-level implementation details of the FFT algorithm offered by the C library FFTW, as well as leveraging cuFFT to move computations to the GPU. In addition, I implemented a high-throughput automated pipelines for segmenting organoids based on a mask-RCNN model. I oversaw a group of students in annotating 3D datasets, and later trained the model, applied it, and analyzed the resulting 3D+t organoid predictions.