Developing an automated microscopy analysis pipeline

The goal is to build a complete pipeline that automates the preprocessing, analysis, and visualization of microscopy data. The pipeline is as follows: Scheduled transfer Microscope -> OSN bucket -> Computation on Bridges-2 GPU: preprocessing with petakit5D (deskew/decon/rotation) -> Segmentation using our refined SAM2 model -> isosurface generation and analysis using u-unwrap3D -> compression/packing of volumetric data into webp and DRACO GLTF for visualization on web viewers. At each stage the intermediate will be stored on the OSN bucket. This will leverage ACCESS allocation BIO240051: Cloud storage and compute for volumetric fluorescence movies