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Amber Herold, 04/23/2010 11:05 AM
Leginon Manual¶
- Table of contents
- Leginon Manual
- An introduction to Leginon
- 1. An introduction to Leginon
- 2. Leginon System version 1.6
- 3. Update to Leginon System version 1.6
- 4. Complete Installation
- 5. Leginon Administration Tools
- 6. Using Project Management Tools
- 7. Installation Troubleshooting
- 8. Microscope Set-up
- 9. Start Leginon
- 10. Leginon "Manual Application"
- 11. Leginon "Calibrations" Application
- 12. Multi-Scale Imaging Applications in General
- 13. Leginon "MSI-Edge" Application
- 14. Leginon "MSI-T" Application
- 15. Leginon "MSI-raster" Application
- 16. Leginon "MSI-RCT" and MSI-RCT raster" Applications
- 17. Leginon "RobotMSI-Section" Application
- 18. Leginon "MSI-Tomography" Application
- 19. Leginon "Robot-MSI-Screen" Applications
- 20. Frequent Asked Questions
- 21. Trouble shooting
- 22. Preferences Setup
- 23. Node Descriptions
- 24. Create and Edit Applications
An introduction to Leginon¶
- What is the Leginon System?
- Terminology
- Graphical User Interface
- Supported Instrument
- Minimum Requirements and current NRAMM setup
- Getting Started
1. An introduction to Leginon¶
- What is the Leginon System?
- Terminology
- Graphical User Interface
- Minimum Requirements and current NRAMM setup
- Getting Started
2. Leginon System version 1.6¶
- pyScope Change
- New User Features
- Updated Applications (All)
- New Project Web Tool Features
- New dbemtool Web Tool Features (1.5.1)
- Bug Fixes
- Recommended Application Preference Changes when updated from version 1.5
- Known Bugs
3. Update to Leginon System version 1.6¶
- Update from v1.1 and v1.2 NOT AVAILABLE
- Update from v1.3-Follow v1.4 update after performing these
- Update from v1.4
- How to Update from v1.5 (Linux)
- Import the new (1.6) applications included with Leginon
- How to Update from v1.5 (Window)
- Additional work at the computer controlling the microscope and camera (Window)
- Recommended Application Preference Changes when updated from version 1.5
4. Complete Installation¶
- Four Parts of the Leginon System
- What is in this Chapter
- Possible Computer Set-up Configurations
- Ports used by Leginon
- Where to register and download Leginon
- Processing Server Installation
- Database Server Installation
- Web Server Installation
- Windows Installation
- Additional installation on the microscope computer
- Next Steps
- 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
- More about Instruments
- Applications
- Calibrations
- Goniometer
6. Using Project Management Tools¶
- Recommendataion-Dividing projects by long-term goal
- Installation
- 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. Microscope Set-up¶
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. Leginon "Calibrations" Application¶
- Importance of making calibrations
- Grids for Calibration
- Startup
- Creating Presets for the first time
- Calibration without presets
- Pixel Size Calibration
- Bright and Dark reference images
- Image Shift matrix calibration
- Beam Shift matrix calibration
- 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
12. 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
- 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
13. Leginon "MSI-Edge" Application¶
- Summary of this application
- Hole Targeting Set-up for MSI-Edge
- Exposure Targeting Set-up for MSI-Edge
14. Leginon "MSI-T" Application¶
15. Leginon "MSI-raster" Application¶
16. Leginon "MSI-RCT" and MSI-RCT raster" Applications¶
17. Leginon "RobotMSI-Section" Application¶
- Summary of this application
- Raster Generation node set-up
- Other special preference set-up
- Tips on Operation
18. Leginon "MSI-Tomography" Application¶
- Summary of this application
- Set-up Before Running
- Running the application
- Full Protocol on a F30 with an energy filter
19. Leginon "Robot-MSI-Screen" Applications¶
- Summary of these applications
- Robot node set-up
- 1st Pass application
- Evaluation application
- 2nd Pass application
- Operation
20. 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?
21. Trouble shooting¶
- Getting Help
- Do and Do Not in leginon
- Pausing and Aborting during data collection
- General operation problems
- Hardware Troubles
- Troubles with Imaging
- Troubles with Targeting
- Troubles with Focusing and Drift Check
- Troubles with Calibrations
- Troubles with Tomography
22. Preferences Setup¶
- Initial MSI application preference setup
- MSI-Tomography Preferences
- Robot MSI-Section preference set-up
23. 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
24. Create and Edit Applications¶
- Use the Application Editor to create Leginon applications
- Reload and Edit an existing application
- 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 Amber Herold over 14 years ago · 27 revisions