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Amber Herold, 04/23/2010 08:32 AM

Leginon Manual

  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 Robot-MSI-Screen Applications
  18. Frequently Asked Questions
  19. Troubleshooting
  20. Initial MSI application preference setup
  21. Node Descriptions
  22. Create and Edit Applications

Contents

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. Leginon System version 1.6

  1. pyScope Change
  2. New User Features
  3. Updated Applications (All)
  4. New Project Web Tool Features
  5. New dbemtool Web Tool Features (1.5.1)
  6. Bug Fixes
  7. Recommended Application Preference Changes when updated from version 1.5
  8. Known Bugs

3. Update to Leginon System version 1.6

  1. Update from v1.1 and v1.2 NOT AVAILABLE
  2. Update from v1.3-Follow v1.4 update after performing these
  3. Update from v1.4
  4. How to Update from v1.5 (Linux)
  5. Import the new (1.6) applications included with Leginon
  6. How to Update from v1.5 (Window)
  7. Additional work at the computer controlling the microscope and camera (Window)
  8. Recommended Application Preference Changes when updated from version 1.5

4. Complete Installation

  1. Four Parts of the Leginon System
  2. What is in this Chapter
  3. Possible Computer Set-up Configurations
  4. Ports used by Leginon
  5. Where to register and download Leginon
  6. Processing Server Installation
  7. Database Server Installation
  8. Web Server Installation
  9. Windows Installation
  10. Additional installation on the microscope computer
  11. Next Steps
  12. 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. More about Instruments
  6. Applications
  7. Calibrations
  8. Goniometer

6. Using Project Management Tools

  1. Recommendataion-Dividing projects by long-term goal
  2. Installation
  3. Go to project tools page
  4. Add a new project
  5. Edit an existing project
  6. 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. Microscope Set-up

  1. Good Alignments Save Time
  2. 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. Leginon "Calibrations" Application

  1. Importance of making calibrations
  2. Grids for Calibration
  3. Startup
  4. Creating Presets for the first time
  5. Calibration without presets
  6. Pixel Size Calibration
  7. Bright and Dark reference images
  8. Image Shift matrix calibration
  9. Beam Shift matrix calibration
  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

12. 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. Queuing option
  13. Queuing Example 1 - Exposure Targeting
  14. Queuing Example 2 - Hole Targeting only
  15. Queuing Example 3 - Both Exposure and Hole Targeting
  16. Monitor Progress of Queued Targets

13. Leginon "MSI-Edge" Application

  1. Summary of this application
  2. Hole Targeting Set-up for MSI-Edge
  3. Exposure Targeting Set-up for MSI-Edge

14. Leginon "MSI-T" Application

  1. Summary of this application
  2. Creating Template
  3. JAHC finder nodes set-up
  4. Queuing Option

15. Leginon "MSI-raster" Application

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

16. Leginon "MSI-RCT" and MSI-RCT raster" Applications

  1. Summary of these applications
  2. RCT node set-up
  3. Presets for MSI-RCT applications

17. 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

18. Leginon "MSI-Tomography" Application

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

19. 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

20. 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?

21. Trouble shooting

  1. Getting Help
  2. Do and Do Not in leginon
  3. Pausing and Aborting during data collection
  4. General operation problems
  5. Hardware Troubles
  6. Troubles with Imaging
  7. Troubles with Targeting
  8. Troubles with Focusing and Drift Check
  9. Troubles with Calibrations
  10. Troubles with Tomography

22. Initial MSI application preference setup

  1. MSI-Tomography Preferences
  2. Robot MSI-Section preference set-up

23. 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

24. Create and Edit Applications

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

Updated by Amber Herold over 14 years ago · 15 revisions