Leginon

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 3.0]]

# [[pyScope Changes 3.0]]

# [[New User Features 3.0]]

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

# [[pyScope Changes 3.1]]

# [[New User Features 3.1]]

h3. 2. 3. [[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. 4. [[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

h3. 2. 5. [[Leginon System version 3.4]]

# [[pyScope Changes 3.4]]

# [[New User Features 3.4]]

# "Bug Fixes":/redmine/projects/leginon/issues?query_id=55

# "Known Bugs":/redmine/projects/leginon/issues?query_id=48

h3. 2. 6. [[Leginon System version 3.5]] (stable)

# [[pyScope Changes 3.5]]

# [[New User Features 3.5]]

# "Bug Fixes":/redmine/projects/leginon/issues?query_id=61

# "Known Bugs":/redmine/projects/leginon/issues?query_id=48

h3. 2. 7. [[Leginon System version 3.6]] (not ready)

# [[pyScope Changes 3.6]]

# [[New User Features 3.6]]

h3. 2.7 [[Leginon System version beta]]

h3. 2.8 [[Leginon System version pymysql]]  This will be used in 3.6 and 4.0 (Python3)

h2. 3. [[Upgrade Instructions]]

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

h3. 3. 2. [[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. 3. [[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. 4. [[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)]]

h3. 3. 5. [[Upgrade to Leginon System version 3.4 from version 3.3]]

# [[How to Update from v3.3 (Linux)]]

# [[How to Update from v3.3 (Instrument Windows Computer)]]

h3. 3. 6. [[Upgrade to Leginon System version 3.5 from version 3.4]]

# [[How to Update from v3.4 (Linux)]]

# [[How to Update from v3.4 (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 [[For the administrators]]

# [[Leginon Administration Tools|Web Leginon Administration Tools]]

# [[Database migrating export/import scripts]]

h2. 5.1  [[Leginon Administration Tools|Web 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]]

h3. [[Efficient way to calibrate matrixes for all mags in the same projection mode]]

# [[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]]

# [[Lens Aberration Correction Calibration for Beam-Image Shift Targeting]]

# [[Dose (Camera Sensitivity) Calibration]]

# [[Check Phase Plate Patches]]

# [[Camera length calibration]] for electron diffraction

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]]

# [[1.9 Å mouse mFth1 recombinant apoferritin image-shift data collection with image-shift aberration-correction ]]

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]]

# [[MSI-T-Tilt Operation|Operation]]

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

h2. 24 [[Lacey Carbon Application]]

*Possible strategies:*

# [[Using MSI-T application to collect Lacey Carbon support data]]

# [[RasterFC Lacey carbon rastering]]

h2. 25. [[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. 26. [[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. 27. [[Preferences Setup]]

# [[Initial MSI application preference setup]]

# [[MSI-Tomography Preferences]]

# [[Robot MSI-Section preference set-up]]

h2. 28. [[Node Descriptions]]

# [[Acquisition]]

# [[AlignZeroLoss]]

# [[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]]

# [[Phase_Plate_Aligner_Node_Class|Phase Plate Aligner]]

# [[Pixel Size Calibrator]]

# [[Presets Manager]]

# [[Raster Finder]]

# [[Raster Filter]]

# [[RCT]]

# [[Robot]]

# [[RobotAtlasTargetFinder]]

# [[Tomography]]

# [[TEM Controller]]

# [[Transform Manager ]]

h2. 28. [[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]]

# [[Import Export Application Settings as json file]]

# [[Create Leginon "Simple Application"]]

# [["Calibrations" Application]]

# [["MSI-Edge" Application]]

# [["MSI-T" Application]]

# [["MSI-raster" Application]]

# [["MSI-Tomography" Application]]

# [["Manual" Application]]