Revision as of 18:46, 20 June 2025

Welcome to the CryoNAV Wiki!

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.

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 of CryoNAV

CryoNAV offers a robust suite of tools to support your cryo-EM research:

Sample & Experiment Management: Define and track sample preparation conditions and experimental parameters.
Tilt Series Data Collection & Import: Interface with microscopes, manage data collection, and import data from various sources.
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.
Data Visualization: View grid atlases, search maps, thumbnails, and inspect raw/processed data.
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:
- IMOD
- Dynamo
- CryoCARE
- DeepDeWedge
- CTFfind
Data Sharing, Uploading & Archiving: Export data, prepare datasets for online repositories (e.g., EMPIAR, EMDB), and manage long-term storage (LTS).

Getting Started

New to CryoNAV? Here are some quick links to get you started:

Navigating This Wiki

Use the navigation menu (usually on the left or top of the page) to explore different sections of this wiki. Key areas include:

Core Concepts & Workflow
CryoNAV Modules & Features (Detailed guides on specific functionalities)
FAQ & Troubleshooting
Community & Support

We hope this wiki helps you make the most of CryoNAV!

@@ Line 1: / Line 1: @@
-<strong>MediaWiki has been installed.</strong>
+{{DISPLAYTITLE:CryoNAV Home}}
+<!-- This is the main landing page for the CryoNAV Wiki -->
-Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.
+= Welcome to the CryoNAV Wiki! =
-== Getting started ==
+'''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.
-* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
-* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
+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.
-* [https://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]
-* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
+== Key Features of CryoNAV ==
-* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
+CryoNAV offers a robust suite of tools to support your cryo-EM research:
+* '''Sample & Experiment Management:''' Define and track sample preparation conditions and experimental parameters.
+* '''Tilt Series Data Collection & Import:''' Interface with microscopes, manage data collection, and import data from various sources.
+* '''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.
+* '''Data Visualization:''' View grid atlases, search maps, thumbnails, and inspect raw/processed data.
+* '''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 ==
+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 ==
+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]]