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Anchi Cheng, 08/12/2014 10:28 AM

Leginon Manual

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

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)

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. Gatan camera configuration
  3. Tietz camera configuration
  4. Good Alignments Save Time
  5. 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 SpecificsI

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

TEM

Camera

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. Stage Position matrix calibration
  10. Modeled Stage Position calibration
  11. Checking Matrix and Modeled Stage Position Calibration
  12. Autofocus Calibration with Beam Tilt Node
  13. 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

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. 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

Updated by Anchi Cheng over 10 years ago · 81 revisions