|
|
| (2 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| {{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!
| |
| | |
| == 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. -->
| |
| | |
| <!-- Categories can help organize pages -->
| |
| [[Category:CryoNAV]]
| |
| [[Category:Documentation]]
| |
| [[Category:Getting Started]]
| |
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:
Founding Agencies
