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Leginon Manual » History » Revision 108

Revision 107 (Anchi Cheng, 01/31/2018 11:21 PM) → Revision 108/137 (Anchi Cheng, 01/31/2018 11:26 PM)

h1. Leginon Manual 

 {{>toc}} 


 h2. 1. [[An introduction to Leginon]] 

 # [[What is the Leginon System?]] 
 # [[Terminology]] 
 # [[Graphical User Interface]] 
 # [[Minimum Requirements and current NRAMM setup]] 
 # [[Getting Started]] 

 h2. 2. [[Version Change Log]] 

 h3. 2. 1. [[Leginon System version 2.2]] 

 # [[pyScope Changes 2.2]] 
 # [[New User Features 2.2]] 

 h3. 2. 2. [[Leginon System version 3.0]] 

 # [[pyScope Changes 3.0]] 
 # [[New User Features 3.0]] 

 h3. 2. 3. [[Leginon System version 3.1]] 

 # [[pyScope Changes 3.1]] 
 # [[New User Features 3.1]] 

 h3. 2. 4. [[Leginon System version 3.2]] 
 # [[pyScope Changes 3.2]] 
 # [[New User Features 3.2]] 
 # "Bug Fixes":/redmine/projects/leginon/issues?query_id=47 
 # "Known Bugs":/redmine/projects/leginon/issues?query_id=48 

 h3. 2. 5. [[Leginon System version 3.3]] 
 # [[pyScope Changes 3.3]] 
 # [[New User Features 3.3]] 
 # "Bug Fixes":/redmine/projects/leginon/issues?query_id=53 
 # "Known Bugs":/redmine/projects/leginon/issues?query_id=48 


 h2. 3. [[Upgrade Instructions]] 

 h3. 3. 1. [[Update within the same version using svn]] 

 h3. 3. 2. [[Upgrade to Leginon System version 2.2 from version 2.1]] 

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

 h3. 3. 3. [[Upgrade to Leginon System version 3.0 from version 2.2]] 

 # [[How to Update from v2.2 (Linux)]] 
 # [[How to Update from v2.2 (Instrument Windows Computer)]] 

 h3. 3. 4. [[Upgrade to Leginon System version 3.0 from version 2.2-redux]] 

 # [[How to Update from v2.2-redux (Linux)]] 
 # [[How to Update from v2.2 (Instrument Windows Computer)|How to Update from v2.2-redux (Instrument Windows Computer)]] 

 h3. 3. 5. [[Upgrade to Leginon System version 3.1 from version 3.0]] 

 # [[How to Update from v3.0 (Linux)]] 
 # [[How to Update from v3.0 (Instrument Windows Computer)]] 

 h3. 3. 6. [[Upgrade to Leginon System version 3.2 from version 3.1]] 

 # [[How to Update from v3.1 (Linux)]] 
 # [[How to Update from v3.1 (Instrument Windows Computer)]] 

 h3. 3. 7. [[Upgrade to Leginon System version 3.3 from version 3.2]] 

 # [[How to Update from v3.2 (Linux)]] 
 # [[How to Update from v3.2 (Instrument Windows Computer)]] 

 h2. 4. [[Complete Installation]] 

 # [[Four Parts of the Leginon System]] 
 # [[What is in this Chapter]] 
 # [[Possible Computer Set-up Configurations]] 
 # [[Network Configuration]] 
 # [[Download Appion Files|Where to register and download Leginon]] 
 # [[Database Server Installation]] 
 # [[Processing Server Installation]] 
 # [[DD Frame Alignment Server Installation]] (only if you have a frame-saving DD camera) 
 # [[Web Server Installation]] 
 # [[Installation_on_the_instrument_computers|Installation on the microscope/camera Windows computer]] 
 # [[Steps involved in the installation| Steps needed for Installation Using Database Administration Tools]] 
 # [[Add a new project for test| Create a test project for testing]] 
 # [[Start Leginon|Perform Microscope Setup and Test run]] 
 # [[Backup Practices]] 

 h2. 5. [[Leginon Administration Tools]] 

 # [[Recommandation_for_setup_at_a_new_institute|Recommendation for setup at a new institute]] 
 # [[Steps involved in the installation]] 
 # [[Set up for a new regular user]] 
 # [[More about Groups]] 
 # [[Default Settings|Revert Settings]] 
 # [[Applications]] 
 # [[Goniometer]] 

 h2. 6. [[Using Project Management Tools]] 

 # [[Recommendataion-Dividing projects by long-term goal|Recommendation-Dividing projects by long-term goal]] 
 # [[Go to project tools page]] 
 # [[Add a new project]] 
 # [[Edit an existing project]] 
 # [[Grid management]] 

 h2. 7. [[TroubleShootInstall|Installation Troubleshooting]] 

 # [[Getting Help]] 
 # [[Installation/Update problems]] 
 # [[Administration Tool problems]] 
 # [[Test run operation problems]] 
 # [[Network problems]] 
 # [[Troubles with Imaging]] 
 # [[Troubles with Calibrations]] 



 h2. 8. [[Instrument Set-up]] 

 # [[Calibrations required on FEI microscopes]] 
 # [[Setup and Calibration for jeol.cfg|Setup jeol.cfg on JEOL JEM microscopes]] 
 # [[Low dose shutter configuration for Gatan camera in Digital Micrograph program|Gatan camera configuration]] 
 # [[Tietz camera configuration]] 
 # [[Good Alignments Save Time]] 
 # [[Microscope Set-up Checklist]] 

 h2. 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]] 

 h2. 10. [[Leginon "Manual Application"]] 

 # [[The Application]] 
 # [[Startup]] 
 # [[Running "Manual" Application]] 
 # [[Advanced Features]] 
 # [[Using the Web viewer]] 

 h2. 11. [[Instrument Usage Specifics]] 

 h3. General 

 # [[Instrument Selection]] 
 # [[Camera Configuration]] 
 # [[Saving Frames from Direct Detectors]] 

 h3. TEM 

 * [[Using FEI Titan Krios in Leginon]] 
 * [[Leginon Operation for JEM scopes|Leginon Operation for JEOL JEM scopes]] 

 h3. Camera 

 * [[Using_DE_DDD_in_Leginon|Direct Electron DE-12 and DE-20]] 
 * [[Using_Falcon_Orius_combo_in_Leginon|FEI Falcon]] 
 * [[Using_Gatan_K2_Summit_in_Leginon|Gatan K2 Summit]] 

 h2. 12. [[Leginon "Calibrations" Application]] 

 # [[Importance of making calibrations]] 
 # [[Grids for Calibration]] 
 # [[Startup Calibrations|Startup]] 
 # [[Creating Presets for the first time]] 
 # [[Pixel Size Calibration]] 
 # [[Bright and Dark reference images]] 
 # [[Image Shift matrix calibration]] 
 # [[Beam Shift matrix calibration]] 
 # [[Image Beam Compensation Calibration]] (JEOL scopes only) 
 # [[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]] 
 # [[Check Phase Plate Patches]] 

 h2. 13. [[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]] 
 # [[Optimizing Autofocus]] 
 # [[Adding a new focus sequence to a focus node]] 
 # [[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]] 
 # [[Iterative Stage Movement|Iterative Stage Movement Option]] 

 h2. 14. [[Data Collection Setup Examples]] 

 # [[Sub-3Å proteasome stage-shift data collection]] 
 # [[Sub-3Å proteasome image-shift data collection]] 

 h2. 15. [[Leginon "MSI-T" Application]] 

 # [[Summary of this application - MSI-T|Summary of this application]] 
 # [[Creating Template]] 
 # [[Hole Targeting Set-up for MSI-T]] 
 # [[Exposure Targeting Set-up for MSI-T]] 

 h2. 16. [[Leginon "MSI-Edge" Application]] 

 # [[Summary of this application]] 
 # [[Edge Hole Finder Set-up]] 

 h2. 17. [[Leginon "MSI-raster" Application]] 

 # [[Summary of this application - MSI-raster|Summary of this application]] 
 # [[raster finder nodes set-up]] 
 # [[Improving Autofocusing]] 

 h2. 18. [[Leginon "MSI-RCT" and MSI-RCT raster" Applications]] 

 # [[Summary of this application - MSI-RCT|Summary of these applications]] 
 # [[RCT node set-up]] 
 # [[Presets for MSI-RCT applications]] 
 # [[RCT calibration]] 
 # [[RCT run protocol from a user]] 

 h2. 19. [[Leginon "RobotMSI-Section" Application]] 

 # [[Summary of this application - RobotMSI|Summary of this application]] 
 # [[Raster Generation node set-up]] 
 # [[Other special preference set-up]] 
 # [[Tips on Operation]] 

 h2. 20. [[Leginon "MSI-Tomography" Application]] 

 # [[Summary of this application - MSI-Tomo|Summary of this application]] 
 # [[Set-up Before Running]] 
 # [[Running the application]] 
 # [[Set up dose parameters in Tomography]] 
 # [[Full Protocol on a F30 with an energy filter]] 

 h2. 21. [[Leginon "Robot-MSI-Screen" Applications]] 

 # [[Summary of this application - Robot-MSI-Screen|Summary of these applications]] 
 # [[Robot node set-up]] 
 # [[1st Pass application]] 
 # [[Evaluation application]] 
 # [[2nd Pass application]] 
 # [[Operation]] 

 h2. 22. [[Leginon "MSI-T-Tilt" Application]] 

 # [[Summary of this application - MSI-T-Tilt|Summary of this application]] 
 # [[MSI-T-Tilt Installation]] 
 # [[Operation]] 

 h2. 23. [[MSI-PP_Appplication|Leginon "MSI-PP" Application]] 

 h2. 24. [[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?]] 

 h2. 25. 24. [[Trouble shooting]] 

 # [[Getting Help - 2|Getting Help]] 
 # [[Do and Do Not in leginon]] 
 # [[Pausing and Aborting during data collection]] 
 # [[Aborting targets that are not yet being processed]] 
 # [[Restarting procedure to continue data acquisition]] 
 # [[General operation problems]] 
 # [[Hardware Troubles]] 
 # [[Troubles with Imaging - Troubleshooting|Troubles with Imaging]] 
 # [[Troubles with Targeting]] 
 # [[Troubles with Focusing and Drift Check]] 
 # [[Troubles with Calibrations - Troubleshooting|Troubles with Calibrations]] 
 # [[Troubles with Tomography]] 

 h2. 26. 25. [[Preferences Setup]] 

 # [[Initial MSI application preference setup]] 
 # [[MSI-Tomography Preferences]] 
 # [[Robot MSI-Section preference set-up]] 

 h2. 27. 26. [[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 ]] 

 h2. 28. 27. [[Create and Edit Applications]] 

 # [[Use the Application Editor to create Leginon applications|Use the Application Editor in Leginon to create or edit Leginon applications]] 
 # [[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]]