Leginon Manual¶

• Table of contents
• Leginon Manual
  • 1. An introduction to Leginon
  • 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
  • 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
    • General
    • TEM
    • Camera
  • 12. Leginon "Calibrations" Application
  • 13. Multi-Scale Imaging Applications in General
  • Data Collection Strategy Combination
  • 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¶

1. What is the Leginon System?
2. Terminology
3. Graphical User Interface
4. Minimum Requirements and current NRAMM setup
5. Getting Started

2. Version Change Log¶

2. 1. Leginon System version 2.2¶

1. pyScope Changes 2.2
2. New User Features 2.2

2. 2. Leginon System version 3.0¶

1. pyScope Changes 3.0
2. New User Features 3.0

2. 3. Leginon System version 3.1¶

1. pyScope Changes 3.1
2. New User Features 3.1

2. 3. Leginon System version 3.2

1. pyScope Changes 3.2
2. New User Features 3.2
3. Bug Fixes
4. Known Bugs

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¶

1. How to Update from v2.1 (Linux)
2. How to Update from v2.1 (Microscope Windows Computer)
3. Check Cs value match before using Leginon after update

3. 3. Upgrade to Leginon System version 3.0 from version 2.2¶

1. How to Update from v2.2 (Linux)
2. How to Update from v2.2 (Instrument Windows Computer)

3. 4. Upgrade to Leginon System version 3.0 from version 2.2-redux¶

1. How to Update from v2.2-redux (Linux)
2. How to Update from v2.2-redux (Instrument Windows Computer)

3. 5. Upgrade to Leginon System version 3.1 from version 3.0¶

1. How to Update from v3.0 (Linux)
2. How to Update from v3.0 (Instrument Windows Computer)

3. 6. Upgrade to Leginon System version 3.2 from version 3.1¶

1. How to Update from v3.1 (Linux)
2. How to Update from v3.1 (Instrument Windows Computer)

4. Complete Installation¶

1. Four Parts of the Leginon System
2. What is in this Chapter
3. Possible Computer Set-up Configurations
4. Network Configuration
5. Where to register and download Leginon
6. Database Server Installation
7. Processing Server Installation
8. DD Frame Alignment Server Installation (only if you have a frame-saving DD camera)
9. Web Server Installation
10. Installation on the microscope/camera Windows computer
11. Steps needed for Installation Using Database Administration Tools
12. Create a test project for testing
13. Perform Microscope Setup and Test run
14. Backup Practices

5. Leginon Administration Tools¶

1. Recommandation for setup at a new institute
2. Steps involved in the installation
3. Set up for a new regular user
4. More about Groups
5. Revert Settings
6. Applications
7. Goniometer

6. Using Project Management Tools¶

1. Recommendataion-Dividing projects by long-term goal
2. Go to project tools page
3. Add a new project
4. Edit an existing project
5. Grid management

7. Installation Troubleshooting¶

1. Getting Help
2. Installation/Update problems
3. Administration Tool problems
4. Test run operation problems
5. Network problems
6. Troubles with Imaging
7. Troubles with Calibrations

8. Instrument Set-up¶

1. Calibrations required on FEI microscopes
2. Setup jeol.cfg on JEOL JEM microscopes
3. Gatan camera configuration
4. Tietz camera configuration
5. Good Alignments Save Time
6. Microscope Set-up Checklist

9. Start Leginon¶

1. Test Leginon with Simulator
2. Test Leginon on the Computer Controlling the Microscope
3. Test Network Connection Between Remote and Microscope Computers
4. Run Leginon Client on the Microscope Computer
5. Start Leginon at your main working station remotely

10. Leginon "Manual Application"¶

1. The Application
2. Startup
3. Running "Manual" Application
4. Advanced Features
5. Using the Web viewer

11. Instrument Usage Specifics¶

General¶

1. Instrument Selection
2. Camera Configuration
3. Saving Frames from Direct Detectors

TEM¶

• Using FEI Titan Krios in Leginon
• Leginon Operation for JEOL JEM scopes

Camera¶

• Direct Electron DE-12 and DE-20
• FEI Falcon
• Gatan K2 Summit

12. Leginon "Calibrations" Application¶

1. Importance of making calibrations
2. Grids for Calibration
3. Startup
4. Creating Presets for the first time
5. Pixel Size Calibration
6. Bright and Dark reference images
7. Image Shift matrix calibration
8. Beam Shift matrix calibration
9. Image Beam Compensation Calibration (JEOL scopes only)
10. Stage Position matrix calibration
11. Modeled Stage Position calibration
12. Checking Matrix and Modeled Stage Position Calibration
13. Autofocus Calibration with Beam Tilt Node
14. Dose (Camera Sensitivity) Calibration

13. Multi-Scale Imaging Applications in General¶

1. Multi-Scale Imaging Concept
2. Ways of Moving to Targets in Nodes that acquire images inside MSI
3. Flavors of MSI applications
4. Summary of MSI applications
5. Pre-MSI Set-up
6. Initial MSI application preferences
7. Special Operation Preference setup
8. MSI Quick-start
9. MSI set-up in more details
10. Special Operation setup
11. MSI Operation
12. Optimizing Autofocus
13. Adding a new focus sequence to a focus node
14. Queuing option
15. Queuing Example 1 - Exposure Targeting
16. Queuing Example 2 - Hole Targeting only
17. Queuing Example 3 - Both Exposure and Hole Targeting
18. Monitor Progress of Queued Targets
19. Iterative Stage Movement Option

Data Collection Strategy Combination¶

1. Sub-3Å proteasome stage-shift data collection
2. Sub-3Å proteasome image-shift data collection

14. Leginon "MSI-T" Application¶

1. Summary of this application
2. Creating Template
3. Hole Targeting Set-up for MSI-T
4. Exposure Targeting Set-up for MSI-T

15. Leginon "MSI-Edge" Application¶

1. Summary of this application
2. Edge Hole Finder Set-up

16. Leginon "MSI-raster" Application¶

1. Summary of this application
2. raster finder nodes set-up
3. Improving Autofocusing

17. Leginon "MSI-RCT" and MSI-RCT raster" Applications¶

1. Summary of these applications
2. RCT node set-up
3. Presets for MSI-RCT applications
4. RCT calibration
5. RCT run protocol from a user

18. Leginon "RobotMSI-Section" Application¶

1. Summary of this application
2. Raster Generation node set-up
3. Other special preference set-up
4. Tips on Operation

19. Leginon "MSI-Tomography" Application¶

1. Summary of this application
2. Set-up Before Running
3. Running the application
4. Set up dose parameters in Tomography
5. Full Protocol on a F30 with an energy filter

20. Leginon "Robot-MSI-Screen" Applications¶

1. Summary of these applications
2. Robot node set-up
3. 1st Pass application
4. Evaluation application
5. 2nd Pass application
6. Operation

21. Frequent Asked Questions¶

1. How does Leginon Name the Files?
2. Why does the first Grid Image Not Numbered 00001?
3. What is the definition of ice thickness in the hole finders?

22. Trouble shooting¶

1. Getting Help
2. Do and Do Not in leginon
3. Pausing and Aborting during data collection
4. Aborting targets that are not yet being processed
5. Restarting procedure to continue data acquisition
6. General operation problems
7. Hardware Troubles
8. Troubles with Imaging
9. Troubles with Targeting
10. Troubles with Focusing and Drift Check
11. Troubles with Calibrations
12. Troubles with Tomography

23. Preferences Setup¶

1. Initial MSI application preference setup
2. MSI-Tomography Preferences
3. Robot MSI-Section preference set-up

24. Node Descriptions¶

1. Acquisition
2. BeamFixer
3. Beam Tilt Calibrator
4. Beam Tilt Imager
5. Click Target Finder
6. Corrector
7. Dose Calibrator
8. Drift Manager
9. The EM node
10. FFT Maker
11. Focuser
12. Gon Modeler
13. Hole Finder
14. Hole Depth
15. JAHC Hole Finder (Template Hole Finder)
16. Manual Acquisition
17. Matlab Target Finder
18. Matrix Calibrator
19. Mosaic Click Target Finder
20. Mosaic Target Maker
21. Navigator
22. Pixel Size Calibrator
23. Presets Manager
24. Raster Finder
25. Raster Filter
26. RCT
27. Robot
28. RobotAtlasTargetFinder
29. Tomography
30. Transform Manager

25. Create and Edit Applications¶

1. Use the Application Editor in Leginon to create or edit Leginon applications
2. Edit an existing application as an xml file
3. Create Leginon "Simple Application"
4. "Calibrations" Application
5. "MSI-Edge" Application
6. "MSI-T" Application
7. "MSI-raster" Application
8. "MSI-Tomography" Application
9. "Manual" Application