Leginon Manual » History » Revision 135
Revision 134 (Anchi Cheng, 09/21/2022 11:38 AM) → Revision 135/137 (Anchi Cheng, 09/21/2022 11:47 AM)
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)]]
h3. 3. 6. [[Upgrade to Leginon System version 3.6 from version 3.5]]
# [[How to Update from v3.5 (Linux)]]
# [[How to Update from v3.5 v3.6 (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]]