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Anchi Cheng, 07/29/2015 12:04 PM
Leginon Manual¶
- Table of contents
- Leginon Manual
- 1. An introduction to Leginon
- 2. Version Change Log
- 3. Upgrade Instructions
- 3. 1. Update within the same version using svn
- 3. 2. Upgrade to Leginon System version 2.2 from version 2.1
- 3. 3. Upgrade to Leginon System version 3.0 from version 2.2
- 3. 4. Upgrade to Leginon System version 3.0 from version 2.2-redux
- 3. 5. Upgrade to Leginon System version 3.1 from version 3.0
- 3. 6. Upgrade to Leginon System version 3.2 from version 3.1
- 4. Complete Installation
- 5. Leginon Administration Tools
- 6. Using Project Management Tools
- 7. Installation Troubleshooting
- 8. Instrument Set-up
- 9. Start Leginon
- 10. Leginon "Manual Application"
- 11. Instrument Usage Specifics
- 12. Leginon "Calibrations" Application
- 13. Multi-Scale Imaging Applications in General
- 14. Leginon "MSI-T" Application
- 15. Leginon "MSI-Edge" Application
- 16. Leginon "MSI-raster" Application
- 17. Leginon "MSI-RCT" and MSI-RCT raster" Applications
- 18. Leginon "RobotMSI-Section" Application
- 19. Leginon "MSI-Tomography" Application
- 20. Leginon "Robot-MSI-Screen" Applications
- 21. Frequent Asked Questions
- 22. Trouble shooting
- 23. Preferences Setup
- 24. Node Descriptions
- 25. Create and Edit Applications
1. An introduction to Leginon¶
- What is the Leginon System?
- Terminology
- Graphical User Interface
- Minimum Requirements and current NRAMM setup
- Getting Started
2. Version Change Log¶
2. 1. Leginon System version 2.2¶
2. 2. Leginon System version 3.0¶
2. 3. Leginon System version 3.1¶
2. 3. Leginon System version 3.2 (Coming soon)¶
3. Upgrade Instructions¶
3. 1. Update within the same version using svn¶
3. 2. Upgrade to Leginon System version 2.2 from version 2.1¶
- How to Update from v2.1 (Linux)
- How to Update from v2.1 (Microscope Windows Computer)
- Check Cs value match before using Leginon after update
3. 3. Upgrade to Leginon System version 3.0 from version 2.2¶
3. 4. Upgrade to Leginon System version 3.0 from version 2.2-redux¶
3. 5. Upgrade to Leginon System version 3.1 from version 3.0¶
3. 6. Upgrade to Leginon System version 3.2 from version 3.1¶
4. Complete Installation¶
- Four Parts of the Leginon System
- What is in this Chapter
- Possible Computer Set-up Configurations
- Network Configuration
- Where to register and download Leginon
- Database Server Installation
- Processing Server Installation
- DD Frame Alignment Server Installation (only if you have a frame-saving DD camera)
- Web Server Installation
- Installation on the microscope/camera Windows computer
- Steps needed for Installation Using Database Administration Tools
- Create a test project for testing
- Perform Microscope Setup and Test run
- Backup Practices
5. Leginon Administration Tools¶
- Recommandation for setup at a new institute
- Steps involved in the installation
- Set up for a new regular user
- More about Groups
- Revert Settings
- Applications
- Goniometer
6. Using Project Management Tools¶
- Recommendataion-Dividing projects by long-term goal
- Go to project tools page
- Add a new project
- Edit an existing project
- Grid management
7. Installation Troubleshooting¶
- Getting Help
- Installation/Update problems
- Administration Tool problems
- Test run operation problems
- Network problems
- Troubles with Imaging
- Troubles with Calibrations
8. Instrument Set-up¶
- Calibrations required on FEI microscopes
- Setup jeol.cfg on JEOL JEM microscopes
- Gatan camera configuration
- Tietz camera configuration
- Good Alignments Save Time
- Microscope Set-up Checklist
9. Start Leginon¶
- Test Leginon with Simulator
- Test Leginon on the Computer Controlling the Microscope
- Test Network Connection Between Remote and Microscope Computers
- Run Leginon Client on the Microscope Computer
- Start Leginon at your main working station remotely
10. Leginon "Manual Application"¶
11. Instrument Usage Specifics¶
General¶
TEM¶
Camera¶
12. Leginon "Calibrations" Application¶
- Importance of making calibrations
- Grids for Calibration
- Startup
- Creating Presets for the first time
- Pixel Size Calibration
- Bright and Dark reference images
- Image Shift matrix calibration
- Beam Shift matrix calibration
- Image Beam Compensation Calibration (JEOL scopes only)
- Stage Position matrix calibration
- Modeled Stage Position calibration
- Checking Matrix and Modeled Stage Position Calibration
- Autofocus Calibration with Beam Tilt Node
- Dose (Camera Sensitivity) Calibration
13. Multi-Scale Imaging Applications in General¶
- Multi-Scale Imaging Concept
- Ways of Moving to Targets in Nodes that acquire images inside MSI
- Flavors of MSI applications
- Summary of MSI applications
- Pre-MSI Set-up
- Initial MSI application preferences
- Special Operation Preference setup
- MSI Quick-start
- MSI set-up in more details
- Special Operation setup
- MSI Operation
- Optimizing Autofocus
- Adding a new focus sequence to a focus node
- Queuing option
- Queuing Example 1 - Exposure Targeting
- Queuing Example 2 - Hole Targeting only
- Queuing Example 3 - Both Exposure and Hole Targeting
- Monitor Progress of Queued Targets
- Iterative Stage Movement Option
14. Leginon "MSI-T" Application¶
- Summary of this application
- Creating Template
- Hole Targeting Set-up for MSI-T
- Exposure Targeting Set-up for MSI-T
15. Leginon "MSI-Edge" Application¶
16. Leginon "MSI-raster" Application¶
17. Leginon "MSI-RCT" and MSI-RCT raster" Applications¶
- Summary of these applications
- RCT node set-up
- Presets for MSI-RCT applications
- RCT calibration
- RCT run protocol from a user
18. Leginon "RobotMSI-Section" Application¶
- Summary of this application
- Raster Generation node set-up
- Other special preference set-up
- Tips on Operation
19. Leginon "MSI-Tomography" Application¶
- Summary of this application
- Set-up Before Running
- Running the application
- Set up dose parameters in Tomography
- Full Protocol on a F30 with an energy filter
20. Leginon "Robot-MSI-Screen" Applications¶
- Summary of these applications
- Robot node set-up
- 1st Pass application
- Evaluation application
- 2nd Pass application
- Operation
21. Frequent Asked Questions¶
- How does Leginon Name the Files?
- Why does the first Grid Image Not Numbered 00001?
- What is the definition of ice thickness in the hole finders?
22. Trouble shooting¶
- Getting Help
- Do and Do Not in leginon
- Pausing and Aborting during data collection
- Aborting targets that are not yet being processed
- Restarting procedure to continue data acquisition
- General operation problems
- Hardware Troubles
- Troubles with Imaging
- Troubles with Targeting
- Troubles with Focusing and Drift Check
- Troubles with Calibrations
- Troubles with Tomography
23. Preferences Setup¶
- Initial MSI application preference setup
- MSI-Tomography Preferences
- Robot MSI-Section preference set-up
24. Node Descriptions¶
- Acquisition
- BeamFixer
- Beam Tilt Calibrator
- Beam Tilt Imager
- Click Target Finder
- Corrector
- Dose Calibrator
- Drift Manager
- The EM node
- FFT Maker
- Focuser
- Gon Modeler
- Hole Finder
- Hole Depth
- JAHC Hole Finder (Template Hole Finder)
- Manual Acquisition
- Matlab Target Finder
- Matrix Calibrator
- Mosaic Click Target Finder
- Mosaic Target Maker
- Navigator
- Pixel Size Calibrator
- Presets Manager
- Raster Finder
- Raster Filter
- RCT
- Robot
- RobotAtlasTargetFinder
- Tomography
- Transform Manager
25. Create and Edit Applications¶
- Use the Application Editor in Leginon to create or edit Leginon applications
- Edit an existing application as an xml file
- Create Leginon "Simple Application"
- "Calibrations" Application
- "MSI-Edge" Application
- "MSI-T" Application
- "MSI-raster" Application
- "MSI-Tomography" Application
- "Manual" Application
Updated by Anchi Cheng over 9 years ago · 89 revisions