Latest revision as of 00:23, 21 June 2025

Welcome to the CryoNAV Wiki! This wiki is designed to guide new users through CryoNAV, a comprehensive software solution for Cryo-Electron Microscopy (Cryo-EM) data management.

About CryoNAV

CryoNAV assists researchers in managing the entire lifecycle of cryo-EM data, including:

Sample preparation conditions
Tilt series data collection
Data retrieval from microscope servers
Comprehensive metadata management
Tracking search maps and thumbnails of grids (and associated tilt series at specific locations)
Secure storage and backup of raw data
Data processing using integrated and external cryo-EM tools (e.g., IMOD, Dynamo, CryoCARE, DeepDeWedge, CTFfind)
Uploading to online repositories and databases
Efficient cataloguing and archiving for Long Term Storage (LTS)

Key Features

End-to-End Data Management: From sample creation to final archiving.
Metadata Richness: Capture and organize all relevant experimental details.
Visualization: Tools for grid and tilt-series visualization.
Integration: Seamless workflow with popular cryo-EM processing software.
Collaboration: Facilitates data sharing and repository submission.
Scalability: Designed for handling large datasets and long-term storage.

Wiki Navigation

Explore the CryoNAV wiki using the following sections. Each link will take you to a dedicated page for that topic:

I. General Information
II. Getting Started with CryoNAV
III. Core Concepts & Workflow in CryoNAV
IV. CryoNAV Modules & Features
V. Data Processing with CryoNAV
VI. Walkthroughs & Workshops

Founding Agencies

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-{{DISPLAYTITLE:CryoNAV Home}}
+{{DISPLAYTITLE:''CryoNAV Wiki Home''}}
-<!-- This is the main landing page for the CryoNAV Wiki -->
-= Welcome to the CryoNAV Wiki! =
+Welcome to the CryoNAV Wiki! This wiki is designed to guide new users through CryoNAV, a comprehensive software solution for Cryo-Electron Microscopy (Cryo-EM) data management.
-'''CryoNAV''' is a comprehensive software solution designed to streamline and manage the entire cryo-electron microscopy (cryo-EM) data lifecycle. This wiki serves as a guide for new and existing CryoNAV users, helping you navigate its features and effectively manage your cryo-EM projects from sample preparation to final archiving.
+== About CryoNAV ==
+CryoNAV assists researchers in managing the entire lifecycle of cryo-EM data, including:
+* Sample preparation conditions
+* Tilt series data collection
+* Data retrieval from microscope servers
+* Comprehensive metadata management
+* Tracking search maps and thumbnails of grids (and associated tilt series at specific locations)
+* Secure storage and backup of raw data
+* Data processing using integrated and external cryo-EM tools (e.g., IMOD, Dynamo, CryoCARE, DeepDeWedge, CTFfind)
+* Uploading to online repositories and databases
+* Efficient cataloguing and archiving for Long Term Storage (LTS)
-Whether you are setting up your first experiment, processing complex datasets, or managing long-term storage, CryoNAV provides the tools you need to enhance productivity and ensure data integrity.
+== Key Features ==
+* '''End-to-End Data Management:''' From sample creation to final archiving.
+* '''Metadata Richness:''' Capture and organize all relevant experimental details.
+* '''Visualization:''' Tools for grid and tilt-series visualization.
+* '''Integration:''' Seamless workflow with popular cryo-EM processing software.
+* '''Collaboration:''' Facilitates data sharing and repository submission.
+* '''Scalability:''' Designed for handling large datasets and long-term storage.
-__TOC__ <!-- This magic word forces the Table of Contents to appear here -->
+== Wiki Navigation ==
+Explore the CryoNAV wiki using the following sections. Each link will take you to a dedicated page for that topic:
-== Key Features of CryoNAV ==
+* '''I. [[CryoNAV_General_Information|General Information]]'''
-CryoNAV offers a robust suite of tools to support your cryo-EM research:
+* '''II. [[CryoNAV_Getting_Started|Getting Started with CryoNAV]]'''
-* '''Sample & Experiment Management:''' Define and track sample preparation conditions and experimental parameters.
+* '''III. [[CryoNAV_Core_Concepts_Workflow|Core Concepts & Workflow in CryoNAV]]'''
-* '''Tilt Series Data Collection & Import:''' Interface with microscopes, manage data collection, and import data from various sources.
+* '''IV. [[CryoNAV_Modules_Features|CryoNAV Modules & Features]]'''
-* '''Comprehensive Metadata Management:''' Automate metadata extraction, manually edit and annotate, and utilize advanced search and filtering. Includes management of search maps and thumbnails for grids and tilt series.
+* '''V. [[CryoNAV_Data_Processing|Data Processing with CryoNAV]]'''
-* '''Data Visualization:''' View grid atlases, search maps, thumbnails, and inspect raw/processed data.
+* '''VI. [[CryoNAV_Walkthroughs_Workshops|Walkthroughs & Workshops]]'''
-* '''Secure Data Storage & Backup:''' Configure storage locations and implement best practices for data backup.
-* '''Integrated Data Processing:''' Manage processing pipelines and integrate with popular cryo-EM tools such as:
-** [[CryoNAV_IMOD_Integration|IMOD]]
-** [[CryoNAV_Dynamo_Integration|Dynamo]]
-** [[CryoNAV_CryoCARE_Integration|CryoCARE]]
-** [[CryoNAV_DeepDeWedge_Integration|DeepDeWedge]]
-** [[CryoNAV_CTFfind_Integration|CTFfind]]
-* '''Data Sharing, Uploading & Archiving:''' Export data, prepare datasets for online repositories (e.g., EMPIAR, EMDB), and manage long-term storage (LTS).
-== Getting Started ==
+= Founding Agencies =
-New to CryoNAV? Here are some quick links to get you started:
-* [[CryoNAV_Installation_Guide|Installation Guide]]
-* [[CryoNAV_Quick_Start_Guide|Quick Start Guide]]
-* [[CryoNAV_User_Interface_Overview|User Interface Overview]]
-* [[CryoNAV_Tutorials|Tutorials & Walkthroughs]]
-== Navigating This Wiki ==
+[[File: Snf_logo_rgb_standard_en_pos.png]]
-Use the navigation menu (usually on the left or top of the page) to explore different sections of this wiki. Key areas include:
-* [[CryoNAV_Core_Concepts|Core Concepts & Workflow]]
-* [[CryoNAV_Modules_Features|CryoNAV Modules & Features]] (Detailed guides on specific functionalities)
-* [[CryoNAV_FAQ|FAQ & Troubleshooting]]
-* [[CryoNAV_Community_Support|Community & Support]]
-We hope this wiki helps you make the most of CryoNAV!
-<!-- Categories can help organize pages -->
-[[Category:CryoNAV]]
-[[Category:Documentation]]
-[[Category:Getting Started]]