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

← Older revision		Revision as of 22:30, 20 May 2026
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	~~The core organizational principle of CryoNAV is a hierarchical data model that directly reflects the physical structure of a cryo-ET experiment.~~		#REDIRECT [[CryoNAV Data Lifecycle]]

	~~== Hierarchy ==~~

	* '''Project''' -- groups related experiments (e.g., a study of a particular protein complex).
	* '''Grid''' -- corresponds to a physical EM grid that was frozen and loaded into the microscope. Each project contains one or more grids.
	* '''Search Map (grid square)''' -- a medium-magnification survey image used to identify promising areas for high-magnification data collection.
	* '''Tilt Series''' -- linked to coordinate positions on search maps, preserving the spatial relationship between where on the grid the data was collected and the resulting images.
	* '''Tomogram''' -- the three-dimensional reconstruction computed from an aligned tilt series.

	This hierarchy maps one-to-one onto the decisions a researcher makes during an experiment: selecting which grids to screen, identifying good squares, choosing positions for tilt series collection, and deciding which series merit full reconstruction. Encoding this structure in the data model enables intuitive navigation, from a grid atlas overview down to individual tilt series thumbnails, while maintaining spatial context at every level.

	~~== Metadata stored per entity ==~~

	~~Each tilt series entity stores not only file paths and processing state but also:~~

	* Acquisition metadata: voltage, pixel size, dose, camera type, tilt range
	* User-assigned quality annotations: star rating, tags

	~~This metadata is extracted automatically during import (see~~ [[~~Tilt Series Data Import\|SmartScan]]) and can be used for filtering and batch selection throughout the interface.~~

	~~== Cryo-FIB integration ==~~

	~~For workflows that involve cryo-focused ion beam (cryo-FIB) milling,~~ CryoNAV extends the data model to link sample preparation with TEM data acquisition. Users can attach images from the FIB-SEM instrument (e.g., Thermo Fisher Aquilos) to the corresponding grid entity. These FIB images are visually associated with the lamellae as they appear in the TEM atlas and search maps, creating a traceable link from sample preparation through to data collection and processing.

	~~This integration allows researchers to:~~

	* Correlate milling conditions (lamella thickness, milling angle, curtaining artifacts) with downstream data quality.
	* Review all information about a grid, from FIB preparation to tomogram, in a single location.

	~~== See also ==~~

	* [[Key Concepts]]
	* [[Sample & Experiment Mgt.]]
	* [[Tilt Series Data ~~Import]]~~

	~~[[Category:Core Concepts~~]]

Admin: Bot edit via cryonavedit.py

2026-05-20T20:19:27Z

Bot edit via cryonavedit.py

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The core organizational principle of CryoNAV is a hierarchical data model that directly reflects the physical structure of a cryo-ET experiment.

== Hierarchy ==

* '''Project''' -- groups related experiments (e.g., a study of a particular protein complex).
* '''Grid''' -- corresponds to a physical EM grid that was frozen and loaded into the microscope. Each project contains one or more grids.
* '''Search Map (grid square)''' -- a medium-magnification survey image used to identify promising areas for high-magnification data collection.
* '''Tilt Series''' -- linked to coordinate positions on search maps, preserving the spatial relationship between where on the grid the data was collected and the resulting images.
* '''Tomogram''' -- the three-dimensional reconstruction computed from an aligned tilt series.

This hierarchy maps one-to-one onto the decisions a researcher makes during an experiment: selecting which grids to screen, identifying good squares, choosing positions for tilt series collection, and deciding which series merit full reconstruction. Encoding this structure in the data model enables intuitive navigation, from a grid atlas overview down to individual tilt series thumbnails, while maintaining spatial context at every level.

== Metadata stored per entity ==

Each tilt series entity stores not only file paths and processing state but also:

* Acquisition metadata: voltage, pixel size, dose, camera type, tilt range
* User-assigned quality annotations: star rating, tags

This metadata is extracted automatically during import (see [[Tilt Series Data Import|SmartScan]]) and can be used for filtering and batch selection throughout the interface.

== Cryo-FIB integration ==

For workflows that involve cryo-focused ion beam (cryo-FIB) milling, CryoNAV extends the data model to link sample preparation with TEM data acquisition. Users can attach images from the FIB-SEM instrument (e.g., Thermo Fisher Aquilos) to the corresponding grid entity. These FIB images are visually associated with the lamellae as they appear in the TEM atlas and search maps, creating a traceable link from sample preparation through to data collection and processing.

This integration allows researchers to:

* Correlate milling conditions (lamella thickness, milling angle, curtaining artifacts) with downstream data quality.
* Review all information about a grid, from FIB preparation to tomogram, in a single location.

== See also ==

* [[Key Concepts]]
* [[Sample & Experiment Mgt.]]
* [[Tilt Series Data Import]]

[[Category:Core Concepts]]

CryoEM Data Lifecycle - Revision history

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

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