CryoNAV Quick Start Guide
A preview of the intended quick-start workflow for CryoNAV. This page will be updated once the platform is released.
Typical session workflow
- Project setup. Create a new project (e.g., "Ribosome Study 2025") and invite team members. Confirm that the compute backends (local and/or SLURM) the project will use are configured by the system administrator.
- Data import. After a data collection session, upload the acquisition root folder. SmartScan automatically detects grids, search maps, and tilt series; parses metadata; and establishes coordinate mapping. An import health summary reports the number of detected entities and flags any issues (missing metadata files, incomplete frame sets). For cryo-FIB experiments, also upload FIB-SEM images (grid overviews, milling progress, final lamella views) and link them to the corresponding grid and search map.
- Initial quality screening. If the facility provided pre-processed data, thumbnails are already available. Browse the grid in card view, scanning motion-corrected frames and alignment residual plots. Tag tilt series with obvious problems (broken ice, contamination) and give them low ratings.
- Batch processing. Select promising tilt series via the filter interface (e.g., "unrated or rating >= 3"), configure parameters for the chain of pipeline steps you want to run (motion correction through reconstruction), pick a compute backend, and submit. Jobs appear on the Jobs page with real-time progress bars.
- Result review and curation. As jobs complete, reconstructed tomogram thumbnails appear. Review orthogonal slices, adjust ratings, and launch 3dmod for detailed inspection. Optionally submit denoising jobs (CryoCARE or DeepDeWedge) on selected reconstructions.
- Export and reporting. Generate a project report for PI review or archival purposes; export a CSV of quality metrics for statistical analysis; create a ZIP bundle containing selected tomograms (e.g., only denoised volumes from highest-rated tilt series) to share with a collaborator.