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	~~A preview of the intended quick-start workflow for CryoNAV. This page will be updated once the platform is released.~~		#REDIRECT [[CryoNAV Quick Start Guide]]

	~~== Typical session workflow ==~~

	~~# '''Project setup.''' Create a new project (e.g., "Ribosome Study 2025"), invite team members, and configure processing and computing templates appropriate for your microscope and cluster.~~
	# '''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"), choose a processing workflow template (motion correction through reconstruction), select a computing template, and submit the batch. 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.

	~~== See also ==~~

	* [[~~Tilt Series Data Import]]~~
	* [[Tomogram Processing Overview]]
	* [[Data Sharing & Archiving]]
	* [[Walkthroughs]]

	~~[[Category:Getting Started~~]]

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2026-05-20T20:19:23Z

Bot edit via cryonavedit.py

New page

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"), invite team members, and configure processing and computing templates appropriate for your microscope and cluster.
# '''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"), choose a processing workflow template (motion correction through reconstruction), select a computing template, and submit the batch. 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.

== See also ==

* [[Tilt Series Data Import]]
* [[Tomogram Processing Overview]]
* [[Data Sharing & Archiving]]
* [[Walkthroughs]]

[[Category:Getting Started]]

Quick Start Guide - Revision history

Admin: Bot edit via cryonavedit.py: redirect to sidebar-target title

Admin: Bot edit via cryonavedit.py