CryoNAV About - Revision history

Admin: Bot edit via cryonavedit.py: migrate to sidebar-target titles

2026-05-20T20:30:03Z

Bot edit via cryonavedit.py: migrate to sidebar-target titles

Admin at 22:00, 20 June 2025

2025-06-20T22:00:28Z

← Older revision		Revision as of 00:00, 21 June 2025
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	CryoNAV is being developed by the Navarro Lab, which applies and advances cryo-electron tomography technologies to image cellular samples. The lab's expertise in implementing and developing computational tools for cryo-electron tomographic data processing directly informs CryoNAV's design and functionality.		CryoNAV is being developed by the Navarro Lab, which applies and advances cryo-electron tomography technologies to image cellular samples. The lab's expertise in implementing and developing computational tools for cryo-electron tomographic data processing directly informs CryoNAV's design and functionality.

	The software is being designed to ~~address~~ the ~~lab's mission to build computational strategies~~ for quantitative analysis of 3D volumes and in situ structure determination, extending these capabilities to the broader cryo-EM community through an accessible data management platform.		The software is being designed to handle the demanding requirements of modern cryo-EM labs for quantitative analysis of 3D volumes and in situ structure determination, extending these capabilities to the broader cryo-EM community through an accessible data management platform.

	~~==Technical Specifications==~~

	~~CryoNAV is being designed to handle the demanding requirements of modern cryo-EM facilities:~~
	* Planned support for high-throughput data collection workflows
	* Scalable storage architecture
	* Web-based interface for remote access
	* Multi-user concurrent access capabilities
	* Integration APIs for third-party tools
	* Cross-platform compatibility

	==Support and Documentation==		==Support and Documentation==

Admin at 21:54, 20 June 2025

2025-06-20T21:54:54Z

← Older revision		Revision as of 23:54, 20 June 2025
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	=About CryoNAV=		=About CryoNAV=

	'''CryoNAV''' is a comprehensive data management software platform ~~designed specifically~~ for cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) workflows. ~~Developed~~ by the Navarro Lab at the University of Lausanne (UNIL), CryoNAV ~~provides~~ researchers with an integrated solution for managing the complete lifecycle of cryo-EM data, from initial sample preparation through final data archiving.		'''CryoNAV''' is a comprehensive data management software platform currently under development for cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) workflows. Being developed by the Navarro Lab at the University of Lausanne (UNIL), CryoNAV aims to provide researchers with an integrated solution for managing the complete lifecycle of cryo-EM data, from initial sample preparation through final data archiving.

	==Overview==		==Overview==

	CryoNAV ~~addresses~~ the complex data management challenges faced by cryo-EM facilities and research laboratories by offering a unified platform that ~~streamlines~~ workflows, ~~ensures~~ data integrity, and ~~facilitates~~ collaboration. The software is built with the understanding that cryo-electron tomography is a structural biology method that can determine the molecular architecture of cellular components and macromolecules in their native biological context.		CryoNAV is being designed to address the complex data management challenges faced by cryo-EM facilities and research laboratories by offering a unified platform that will streamline workflows, ensure data integrity, and facilitate collaboration.

	==Key Features==		==Key Features==
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	===Data Collection and Import===		===Data Collection and Import===
	* ~~Automated~~ tilt series data import from microscope servers		* Planned automated tilt series data import from microscope servers
	* Real-time data retrieval and organization		* Real-time data retrieval and organization
	* Support for multiple data collection schemes		* Support for multiple data collection schemes
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	===Data Processing Integration===		===Data Processing Integration===
	CryoNAV ~~integrates~~ with leading cryo-EM processing tools including:		CryoNAV is planned to integrate with leading cryo-EM processing tools including:
	* '''IMOD''' - Image processing and 3D reconstruction		* '''IMOD''' - Image processing and 3D reconstruction
	* '''Dynamo''' - ~~Subtomogram averaging (the lab contributes to the software package Dynamo for subtomogram averaging)~~		* '''Dynamo''' - Image processing and 3D reconstruction
	* '''CryoCARE''' - Content-aware image restoration		* '''CryoCARE''' - Content-aware image restoration
	* '''DeepDeWedge''' - Missing wedge restoration using deep learning		* '''DeepDeWedge''' - Missing wedge restoration using deep learning
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	===Storage and Backup===		===Storage and Backup===
	* ~~Automated~~ data storage management		* Planned automated data storage management
	* Redundant backup systems		* Redundant backup systems
	* Long-term storage (LTS) integration		* Long-term storage (LTS) integration
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	===Sharing and Archiving===		===Sharing and Archiving===
	* ~~Upload~~ capabilities to online repositories and databases		* Planned upload capabilities to online repositories and databases
	* Cataloguing systems for easy data retrieval		* Cataloguing systems for easy data retrieval
	* Long-term archiving solutions		* Long-term archiving solutions
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	==Development Background==		==Development Background==

	CryoNAV ~~was~~ developed by the Navarro Lab, which applies and advances cryo-electron tomography technologies to image cellular samples. The lab's expertise in implementing and developing computational tools for cryo-electron tomographic data processing ~~and subtomogram averaging~~ directly informs CryoNAV's design and functionality.		CryoNAV is being developed by the Navarro Lab, which applies and advances cryo-electron tomography technologies to image cellular samples. The lab's expertise in implementing and developing computational tools for cryo-electron tomographic data processing directly informs CryoNAV's design and functionality.

	The software ~~addresses~~ the lab's mission to build computational strategies for quantitative analysis of 3D volumes and in situ structure determination, extending these capabilities to the broader cryo-EM community through an accessible data management platform.		The software is being designed to address the lab's mission to build computational strategies for quantitative analysis of 3D volumes and in situ structure determination, extending these capabilities to the broader cryo-EM community through an accessible data management platform.

	==Technical Specifications==		==Technical Specifications==

	CryoNAV is designed to handle the demanding requirements of modern cryo-EM facilities:		CryoNAV is being designed to handle the demanding requirements of modern cryo-EM facilities:
	* ~~Support~~ for high-throughput data collection workflows		* Planned support for high-throughput data collection workflows
	* Scalable storage architecture		* Scalable storage architecture
	* Web-based interface for remote access		* Web-based interface for remote access
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	* Integration APIs for third-party tools		* Integration APIs for third-party tools
	* Cross-platform compatibility		* Cross-platform compatibility

	~~==Applications==~~

	~~CryoNAV is particularly well-suited for:~~
	* Academic cryo-EM facilities
	* Core imaging centers
	* Collaborative research projects
	* Training and educational programs

	~~The software supports both single-particle analysis and cryo-electron tomography workflows, making it versatile for various research applications in structural biology.~~

	==Support and Documentation==		==Support and Documentation==
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	==Contact==		==Contact==

	For more information about CryoNAV or to discuss ~~implementation at your facility~~, please contact ~~the development team through~~ the Navarro Lab at UNIL.		For more information about CryoNAV development or to discuss the project, please contact Paula Navarro (paula.navarro{at}unil.ch) at the Navarro Lab, UNIL.

	==See Also==		==See Also==

Admin at 21:42, 20 June 2025

2025-06-20T21:42:29Z

← Older revision		Revision as of 23:42, 20 June 2025
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	* Academic cryo-EM facilities		* Academic cryo-EM facilities
	* Core imaging centers		* Core imaging centers
	* Industrial research laboratories
	* Collaborative research projects		* Collaborative research projects
	* Training and educational programs		* Training and educational programs

Admin: Created page with "=About CryoNAV= '''CryoNAV''' is a comprehensive data management software platform designed specifically for cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) workflows. Developed by the Navarro Lab at the University of Lausanne (UNIL), CryoNAV provides researchers with an integrated solution for managing the complete lifecycle of cryo-EM data, from initial sample preparation through final data archiving. ==Overview== CryoNAV addresses the comp..."

2025-06-20T21:40:17Z

Created page with "=About CryoNAV= '''CryoNAV''' is a comprehensive data management software platform designed specifically for cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) workflows. Developed by the Navarro Lab at the University of Lausanne (UNIL), CryoNAV provides researchers with an integrated solution for managing the complete lifecycle of cryo-EM data, from initial sample preparation through final data archiving. ==Overview== CryoNAV addresses the comp..."

New page

=About CryoNAV=

'''CryoNAV''' is a comprehensive data management software platform designed specifically for cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) workflows. Developed by the Navarro Lab at the University of Lausanne (UNIL), CryoNAV provides researchers with an integrated solution for managing the complete lifecycle of cryo-EM data, from initial sample preparation through final data archiving.

==Overview==

CryoNAV addresses the complex data management challenges faced by cryo-EM facilities and research laboratories by offering a unified platform that streamlines workflows, ensures data integrity, and facilitates collaboration. The software is built with the understanding that cryo-electron tomography is a structural biology method that can determine the molecular architecture of cellular components and macromolecules in their native biological context.

==Key Features==

===Sample and Experiment Management===
* Comprehensive tracking of sample preparation conditions
* Experimental parameter recording and management
* Protocol standardization and documentation

===Data Collection and Import===
* Automated tilt series data import from microscope servers
* Real-time data retrieval and organization
* Support for multiple data collection schemes

===Metadata Management===
* Centralized metadata storage and organization
* Standardized annotation systems
* Cross-referencing capabilities between experiments

===Grid Visualization and Mapping===
* Interactive grid maps and thumbnails
* Location-based tilt series organization
* Visual tracking of data collection progress
* Search functionality for specific grid locations

===Data Processing Integration===
CryoNAV integrates with leading cryo-EM processing tools including:
* '''IMOD''' - Image processing and 3D reconstruction
* '''Dynamo''' - Subtomogram averaging (the lab contributes to the software package Dynamo for subtomogram averaging)
* '''CryoCARE''' - Content-aware image restoration
* '''DeepDeWedge''' - Missing wedge restoration using deep learning
* '''CTFfind''' - Contrast transfer function estimation
* And many other specialized cryo-EM tools

===Storage and Backup===
* Automated data storage management
* Redundant backup systems
* Long-term storage (LTS) integration
* Data integrity verification

===Sharing and Archiving===
* Upload capabilities to online repositories and databases
* Cataloguing systems for easy data retrieval
* Long-term archiving solutions
* Collaboration tools for multi-user access

==Development Background==

CryoNAV was developed by the Navarro Lab, which applies and advances cryo-electron tomography technologies to image cellular samples. The lab's expertise in implementing and developing computational tools for cryo-electron tomographic data processing and subtomogram averaging directly informs CryoNAV's design and functionality.

The software addresses the lab's mission to build computational strategies for quantitative analysis of 3D volumes and in situ structure determination, extending these capabilities to the broader cryo-EM community through an accessible data management platform.

==Technical Specifications==

CryoNAV is designed to handle the demanding requirements of modern cryo-EM facilities:
* Support for high-throughput data collection workflows
* Scalable storage architecture
* Web-based interface for remote access
* Multi-user concurrent access capabilities
* Integration APIs for third-party tools
* Cross-platform compatibility

==Applications==

CryoNAV is particularly well-suited for:
* Academic cryo-EM facilities
* Core imaging centers
* Industrial research laboratories
* Collaborative research projects
* Training and educational programs

The software supports both single-particle analysis and cryo-electron tomography workflows, making it versatile for various research applications in structural biology.

==Support and Documentation==

For installation guides, tutorials, and technical support, please refer to the other sections of this wiki:
* [[Getting Started Home|Getting Started]]
* [[Installation Guide]]
* [[Quick Start Guide]]
* [[Modules & Features Home|Modules & Features]]
* [[Walkthroughs & Workshops Home|Walkthroughs & Workshops]]

==Contact==

For more information about CryoNAV or to discuss implementation at your facility, please contact the development team through the Navarro Lab at UNIL.

==See Also==
* [[Core Concepts Home|Core Concepts & Workflow]]
* [[CryoEM Data Lifecycle]]
* [[Data Processing Home|Data Processing]]
* [[Integration with Cryo-EM Tools]]

[[Category:CryoNAV]]
[[Category:Software]]
[[Category:Cryo-EM]]
[[Category:Data Management]]