Facility-Scale Workflows for Data Acquisition, Standardization, Machine Learning Analysis, and Reproducible Science

Scientific user facilities routinely generate large-scale microscopy datasets across diverse instruments and vendors, differing substantially in file formats, dimensionality, and resolution. Beyond these inconsistencies, datasets are frequently fragmented living across isolated instruments and constrained by security policies and uneven metadata practices. Consequently, tracking, standardizing, processing, and visualizing these datasets in a manner compatible with modern machine learning and autonomous experimentation workflows remains a major challenge. While existing initiatives address data archiving, standardization, or analysis individually, few provide integrated solutions that bridge instrument-level acquisition and scalable ML workflows within heterogeneous, security-constrained user facilities. Here, we establish a deployable, facility-scale infrastructure that bridges instrument-level data generation with cloud-based ML analytics while remaining compliant with institutional n