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Anchi Cheng, 10/15/2019 06:18 PM

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 3.0

  1. pyScope Changes 3.0
  2. New User Features 3.0

2. 2. 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

2. 4. Leginon System version 3.3
  1. pyScope Changes 3.3
  2. New User Features 3.3
  3. Bug Fixes
  4. Known Bugs

2. 5. Leginon System version 3.4 (stable)
  1. pyScope Changes 3.4
  2. New User Features 3.4
  3. Bug Fixes
  4. Known Bugs

2. 5. Leginon System version 3.5 (features can be found in myami-beta branch)
  1. pyScope Changes 3.5
  2. New User Features 3.5
  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 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. 3. 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)

3. 4. Upgrade to Leginon System version 3.3 from version 3.2

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

3. 5. Upgrade to Leginon System version 3.4 from version 3.3

  1. How to Update from v3.3 (Linux)
  2. How to Update from v3.3 (Instrument Windows Computer)

3. 6. Upgrade to Leginon System version 3.4 from version 3.3

  1. How to Update from v3.4 (Linux)
  2. How to Update from v3.4 (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. Recommendation 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. Recommendation-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

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. 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. Lens Aberration Correction Calibration for Beam-Image Shift Targeting
  15. Dose (Camera Sensitivity) Calibration
  16. Check Phase Plate Patches

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. Data Collection Setup Examples

  1. Sub-3Å proteasome stage-shift data collection
  2. Sub-3Å proteasome image-shift data collection
  3. 1.9 Å mouse mFth1 recombinant apoferritin image-shift data collection with image-shift aberration-correction

15. 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

16. Leginon "MSI-Edge" Application

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

17. Leginon "MSI-raster" Application

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

18. 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

19. 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

20. 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

21. 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

22. Leginon "MSI-T-Tilt" Application

  1. Summary of this application
  2. MSI-T-Tilt Installation
  3. Operation

23. Leginon "MSI-PP" Application

24 Lacey Carbon Application

Possible strategies:

  1. Using MSI-T application to collect Lacey Carbon support data
  2. RasterFC Lacey carbon rastering

25. 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?

26. 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

27. Preferences Setup

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

28. Node Descriptions

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

28. 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. Import Export Application Settings as json 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 Anchi Cheng about 5 years ago · 126 revisions