CryoNAV About: Difference between revisions
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=About CryoNAV= | =About CryoNAV= | ||
'''CryoNAV''' is a comprehensive data management software platform | '''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 | 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=== | ||
* | * 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 | 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''' - | * '''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=== | ||
* | * 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=== | ||
* | * 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 | ||
| Line 53: | Line 53: | ||
==Development Background== | ==Development Background== | ||
CryoNAV | 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 | 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: | ||
* | * 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 | ||
| Line 66: | Line 66: | ||
* Integration APIs for third-party tools | * Integration APIs for third-party tools | ||
* Cross-platform compatibility | * Cross-platform compatibility | ||
==Support and Documentation== | ==Support and Documentation== | ||
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==Contact== | ==Contact== | ||
For more information about CryoNAV or to discuss | 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== | ||
Revision as of 23:54, 20 June 2025
About CryoNAV
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
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
Sample and Experiment Management
- Comprehensive tracking of sample preparation conditions
- Experimental parameter recording and management
- Protocol standardization and documentation
Data Collection and Import
- Planned 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 is planned to integrate with leading cryo-EM processing tools including:
- IMOD - Image processing and 3D reconstruction
- Dynamo - Image processing and 3D reconstruction
- 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
- Planned automated data storage management
- Redundant backup systems
- Long-term storage (LTS) integration
- Data integrity verification
Sharing and Archiving
- Planned 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 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.
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
For installation guides, tutorials, and technical support, please refer to the other sections of this wiki:
Contact
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.