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Revision as of 19:03, 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.

III. Core concepts & workflow in CryoNAV

Cryo EM data lifecycle with CryoNAV

Key concepts in CryoNAV

V. Data Processing with CryoNAV

Overview of tomogram processing

Integration with Cryo-EM tools

VI. Walkthroughs & Workshops

Walkthroughs

Workshops

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!

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 __TOC__ <!-- This magic word forces the Table of Contents to appear here -->
+== I. General Information ==
+=== [[CryoNAV_Main_Page|Main page]] ===
+<!-- This link will point to the main page itself. Content for the main page is typically on this page. -->
+=== [[CryoNAV_About|About CryoNAV]] ===
+<!-- Create a page named 'CryoNAV_About' with details about CryoNAV. -->
+=== [[CryoNAV_News_And_Announcements|News & announcements]] ===
+<!-- Create a page named 'CryoNAV_News_And_Announcements' for updates. -->
+== II. Getting Started with CryoNAV ==
+=== [[CryoNAV_Downloads|Download]] ===
+<!-- Create a page named 'CryoNAV_Downloads' with download links and information. -->
+=== [[CryoNAV_Installation_Guide|Installation guide]] ===
+<!-- Create a page named 'CryoNAV_Installation_Guide' with installation instructions. This page might already exist or be planned. -->
+=== [[CryoNAV_Quick_Start_Guide|Quick start guide]] ===
+<!-- Create a page named 'CryoNAV_Quick_Start_Guide' for a first-time user tutorial. This page might already exist or be planned. -->
+== III. Core concepts & workflow in CryoNAV ==
+=== [[CryoNAV_Data_Lifecycle|Cryo EM data lifecycle with CryoNAV]] ===
+<!-- Create a page named 'CryoNAV_Data_Lifecycle' explaining the data workflow. -->
+=== [[CryoNAV_Key_Concepts|Key concepts in CryoNAV]] ===
+<!-- Create a page named 'CryoNAV_Key_Concepts' explaining fundamental CryoNAV entities. -->
+== IV. CryoNAV modules & features ==
+=== [[CryoNAV_Sample_Experiment_Management|Sample & experiment management]] ===
+<!-- Create a page named 'CryoNAV_Sample_Experiment_Management' detailing this feature. -->
+=== [[CryoNAV_Tilt_Series_Data_Collection_Import|Tilt series data collection & import]] ===
+<!-- Create a page named 'CryoNAV_Tilt_Series_Data_Collection_Import' detailing this feature. -->
+=== [[CryoNAV_Metadata_Management|Metadata management]] ===
+<!-- Create a page named 'CryoNAV_Metadata_Management' detailing this feature. -->
+=== [[CryoNAV_Grid_Visualization_Tools|Grid visualization tools]] ===
+<!-- Create a page named 'CryoNAV_Grid_Visualization_Tools' detailing visualization capabilities. -->
+=== [[CryoNAV_Data_Storage_Backup|Data storage & backup]] ===
+<!-- Create a page named 'CryoNAV_Data_Storage_Backup' detailing storage and backup features. -->
+=== [[CryoNAV_Data_Sharing_Archiving|Data sharing & archiving]] ===
+<!-- Create a page named 'CryoNAV_Data_Sharing_Archiving' detailing sharing and archiving. -->
+== V. Data Processing with CryoNAV ==
+=== [[CryoNAV_Tomogram_Processing_Overview|Overview of tomogram processing]] ===
+<!-- Create a page named 'CryoNAV_Tomogram_Processing_Overview' for processing workflows. -->
+=== [[CryoNAV_Tool_Integration|Integration with Cryo-EM tools]] ===
+<!-- Create a page named 'CryoNAV_Tool_Integration' explaining how CryoNAV works with tools like IMOD, Dynamo, etc. You might link to sub-pages for each tool from here. -->
+== VI. Walkthroughs & Workshops ==
+=== [[CryoNAV_Walkthroughs|Walkthroughs]] ===
+<!-- Create a page named 'CryoNAV_Walkthroughs' for step-by-step tutorials. This might consolidate or link to existing tutorials. -->
+=== [[CryoNAV_Workshops|Workshops]] ===
+<!-- Create a page named 'CryoNAV_Workshops' for information on past or upcoming workshops. -->
 == Key Features of CryoNAV ==