Workflow 2D Smartscope

Version 1

Automated screening monitoring workflow designed to provide real-time feedback to the microscope during data acquisition. The pipeline processes movies on-the-fly, performing motion correction, maxshift analysis, CTF estimation and consensus validation, as well as micrograph quality assessment through AI-based categorization. The workflow also includes particle picking, automatic box size estimation, particle extraction, streaming 2D classification, and 2D class quality assessment. Results are integrated into a feedback system that can guide acquisition decisions and optimize screening efficiency in real time. The list of plugins required are: pwem, xmipp3, motioncorr, miffi, cistem, smartscope, sphire, cryoassess.