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Leginon Manual » History » Version 126

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

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h1. Leginon Manual
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{{>toc}}
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h2. 1. [[An introduction to Leginon]]
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# [[What is the Leginon System?]]
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# [[Terminology]]
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# [[Graphical User Interface]]
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# [[Minimum Requirements and current NRAMM setup]]
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# [[Getting Started]]
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h2. 2. [[Version Change Log]]
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h3. 2. 1. [[Leginon System version 3.0]]
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# [[pyScope Changes 3.0]]
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# [[New User Features 3.0]]
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h3. 2. 2. [[Leginon System version 3.1]]
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# [[pyScope Changes 3.1]]
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# [[New User Features 3.1]]
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h3. 2. 3. [[Leginon System version 3.2]]
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# [[pyScope Changes 3.2]]
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# [[New User Features 3.2]]
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# "Bug Fixes":/redmine/projects/leginon/issues?query_id=47
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# "Known Bugs":/redmine/projects/leginon/issues?query_id=48
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h3. 2. 4. [[Leginon System version 3.3]]
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# [[pyScope Changes 3.3]]
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# [[New User Features 3.3]]
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# "Bug Fixes":/redmine/projects/leginon/issues?query_id=53
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# "Known Bugs":/redmine/projects/leginon/issues?query_id=48
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h3. 2. 5. [[Leginon System version 3.4]] (stable)
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# [[pyScope Changes 3.4]]
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# [[New User Features 3.4]]
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# "Bug Fixes":/redmine/projects/leginon/issues?query_id=55
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# "Known Bugs":/redmine/projects/leginon/issues?query_id=48
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h3. 2. 5. [[Leginon System version 3.5]] (features can be found in myami-beta branch)
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# [[pyScope Changes 3.5]]
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# [[New User Features 3.5]]
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# "Bug Fixes":/redmine/projects/leginon/issues?query_id=61
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# "Known Bugs":/redmine/projects/leginon/issues?query_id=48
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h2. 3. [[Upgrade Instructions]]
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h3. 3. 1. [[Update within the same version using svn]]
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h3. 3. 2. [[Upgrade to Leginon System version 3.1 from version 3.0]]
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# [[How to Update from v3.0 (Linux)]]
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# [[How to Update from v3.0 (Instrument Windows Computer)]]
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h3. 3. 3. [[Upgrade to Leginon System version 3.2 from version 3.1]]
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# [[How to Update from v3.1 (Linux)]]
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# [[How to Update from v3.1 (Instrument Windows Computer)]]
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h3. 3. 4. [[Upgrade to Leginon System version 3.3 from version 3.2]]
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# [[How to Update from v3.2 (Linux)]]
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# [[How to Update from v3.2 (Instrument Windows Computer)]]
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h3. 3. 5. [[Upgrade to Leginon System version 3.4 from version 3.3]]
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# [[How to Update from v3.3 (Linux)]]
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# [[How to Update from v3.3 (Instrument Windows Computer)]]
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h3. 3. 6. [[Upgrade to Leginon System version 3.4 from version 3.3]]
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# [[How to Update from v3.4 (Linux)]]
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# [[How to Update from v3.4 (Instrument Windows Computer)]]
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h2. 4. [[Complete Installation]]
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# [[Four Parts of the Leginon System]]
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# [[What is in this Chapter]]
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# [[Possible Computer Set-up Configurations]]
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# [[Network Configuration]]
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# [[Download Appion Files|Where to register and download Leginon]]
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# [[Database Server Installation]]
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# [[Processing Server Installation]]
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# [[DD Frame Alignment Server Installation]] (only if you have a frame-saving DD camera)
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# [[Web Server Installation]]
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# [[Installation_on_the_instrument_computers|Installation on the microscope/camera Windows computer]]
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# [[Steps involved in the installation| Steps needed for Installation Using Database Administration Tools]]
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# [[Add a new project for test| Create a test project for testing]]
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# [[Start Leginon|Perform Microscope Setup and Test run]]
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# [[Backup Practices]]
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h2. 5. [[Leginon Administration Tools]]
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# [[Recommandation_for_setup_at_a_new_institute|Recommendation for setup at a new institute]]
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# [[Steps involved in the installation]]
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# [[Set up for a new regular user]]
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# [[More about Groups]]
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# [[Default Settings|Revert Settings]]
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# [[Applications]]
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# [[Goniometer]]
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h2. 6. [[Using Project Management Tools]]
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# [[Recommendataion-Dividing projects by long-term goal|Recommendation-Dividing projects by long-term goal]]
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# [[Go to project tools page]]
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# [[Add a new project]]
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# [[Edit an existing project]]
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# [[Grid management]]
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h2. 7. [[TroubleShootInstall|Installation Troubleshooting]]
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# [[Getting Help]]
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# [[Installation/Update problems]]
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# [[Administration Tool problems]]
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# [[Test run operation problems]]
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# [[Network problems]]
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# [[Troubles with Imaging]]
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# [[Troubles with Calibrations]]
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h2. 8. [[Instrument Set-up]]
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# [[Calibrations required on FEI microscopes]]
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# [[Setup and Calibration for jeol.cfg|Setup jeol.cfg on JEOL JEM microscopes]]
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# [[Low dose shutter configuration for Gatan camera in Digital Micrograph program|Gatan camera configuration]]
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# [[Tietz camera configuration]]
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# [[Good Alignments Save Time]]
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# [[Microscope Set-up Checklist]]
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h2. 9. [[Start Leginon]]
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# [[Test Leginon with Simulator]]
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# [[Test Leginon on the Computer Controlling the Microscope]]
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# [[Test Network Connection Between Remote and Microscope Computers]]
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# [[Run Leginon Client on the Microscope Computer]]
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# [[Start Leginon at your main working station remotely]]
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h2. 10. [[Leginon "Manual Application"]]
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# [[The Application]]
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# [[Startup]]
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# [[Running "Manual" Application]]
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# [[Advanced Features]]
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# [[Using the Web viewer]]
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h2. 11. [[Instrument Usage Specifics]]
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h3. General
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# [[Instrument Selection]]
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# [[Camera Configuration]]
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# [[Saving Frames from Direct Detectors]]
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h3. TEM
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* [[Using FEI Titan Krios in Leginon]]
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* [[Leginon Operation for JEM scopes|Leginon Operation for JEOL JEM scopes]]
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h3. Camera
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* [[Using_DE_DDD_in_Leginon|Direct Electron DE-12 and DE-20]]
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* [[Using_Falcon_Orius_combo_in_Leginon|FEI Falcon]]
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* [[Using_Gatan_K2_Summit_in_Leginon|Gatan K2 Summit]]
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h2. 12. [[Leginon "Calibrations" Application]]
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# [[Importance of making calibrations]]
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# [[Grids for Calibration]]
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# [[Startup Calibrations|Startup]]
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# [[Creating Presets for the first time]]
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# [[Pixel Size Calibration]]
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# [[Bright and Dark reference images]]
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# [[Image Shift matrix calibration]]
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# [[Beam Shift matrix calibration]]
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# [[Image Beam Compensation Calibration]] (JEOL scopes only)
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# [[Stage Position matrix calibration]]
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# [[Modeled Stage Position calibration]]
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# [[Checking Matrix and Modeled Stage Position Calibration]]
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# [[Autofocus Calibration with Beam Tilt Node]]
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# [[Lens Aberration Correction Calibration for Beam-Image Shift Targeting]]
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# [[Dose (Camera Sensitivity) Calibration]]
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# [[Check Phase Plate Patches]]
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h2. 13. [[Multi-Scale Imaging Applications in General]]
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# [[Multi-Scale Imaging Concept]]
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# [[Ways of Moving to Targets in Nodes that acquire images inside MSI]]
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# [[Flavors of MSI applications]]
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# [[Summary of MSI applications]]
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# [[Pre-MSI Set-up]]
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# [[Initial MSI application preferences]]
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# [[Special Operation Preference setup]]
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# [[MSI Quick-start]]
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# [[MSI set-up in more details]]
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# [[Special Operation setup]]
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# [[MSI Operation]]
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# [[Optimizing Autofocus]]
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# [[Adding a new focus sequence to a focus node]]
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# [[Queuing option]]
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# [[Queuing Example 1 - Exposure Targeting]]
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# [[Queuing Example 2 - Hole Targeting only]]
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# [[Queuing Example 3 - Both Exposure and Hole Targeting]]
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# [[Monitor Progress of Queued Targets]]
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# [[Iterative Stage Movement|Iterative Stage Movement Option]]
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h2. 14. [[Data Collection Setup Examples]]
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# [[Sub-3Å proteasome stage-shift data collection]]
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# [[Sub-3Å proteasome image-shift data collection]]
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# [[1.9 Å mouse mFth1 recombinant apoferritin image-shift data collection with image-shift aberration-correction ]]
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h2. 15. [[Leginon "MSI-T" Application]]
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# [[Summary of this application - MSI-T|Summary of this application]]
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# [[Creating Template]]
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# [[Hole Targeting Set-up for MSI-T]]
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# [[Exposure Targeting Set-up for MSI-T]]
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h2. 16. [[Leginon "MSI-Edge" Application]]
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# [[Summary of this application]]
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# [[Edge Hole Finder Set-up]]
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h2. 17. [[Leginon "MSI-raster" Application]]
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# [[Summary of this application - MSI-raster|Summary of this application]]
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# [[raster finder nodes set-up]]
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# [[Improving Autofocusing]]
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h2. 18. [[Leginon "MSI-RCT" and MSI-RCT raster" Applications]]
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# [[Summary of this application - MSI-RCT|Summary of these applications]]
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# [[RCT node set-up]]
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# [[Presets for MSI-RCT applications]]
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# [[RCT calibration]]
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# [[RCT run protocol from a user]]
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h2. 19. [[Leginon "RobotMSI-Section" Application]]
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# [[Summary of this application - RobotMSI|Summary of this application]]
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# [[Raster Generation node set-up]]
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# [[Other special preference set-up]]
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# [[Tips on Operation]]
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h2. 20. [[Leginon "MSI-Tomography" Application]]
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# [[Summary of this application - MSI-Tomo|Summary of this application]]
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# [[Set-up Before Running]]
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# [[Running the application]]
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# [[Set up dose parameters in Tomography]]
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# [[Full Protocol on a F30 with an energy filter]]
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h2. 21. [[Leginon "Robot-MSI-Screen" Applications]]
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# [[Summary of this application - Robot-MSI-Screen|Summary of these applications]]
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# [[Robot node set-up]]
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# [[1st Pass application]]
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# [[Evaluation application]]
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# [[2nd Pass application]]
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# [[Operation]]
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h2. 22. [[Leginon "MSI-T-Tilt" Application]]
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# [[Summary of this application - MSI-T-Tilt|Summary of this application]]
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# [[MSI-T-Tilt Installation]]
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# [[MSI-T-Tilt Operation|Operation]]
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h2. 23. [[MSI-PP_Appplication|Leginon "MSI-PP" Application]]
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h2. 24 [[Lacey Carbon Application]]
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*Possible strategies:*
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# [[Using MSI-T application to collect Lacey Carbon support data]]
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# [[RasterFC Lacey carbon rastering]]
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h2. 25. [[Frequent Asked Questions]]
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# [[How does Leginon Name the Files?]]
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# [[Why does the first Grid Image Not Numbered 00001?]]
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# [[What is the definition of ice thickness in the hole finders?]]
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h2. 26. [[Trouble shooting]]
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# [[Getting Help - 2|Getting Help]]
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# [[Do and Do Not in leginon]]
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# [[Pausing and Aborting during data collection]]
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# [[Aborting targets that are not yet being processed]]
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# [[Restarting procedure to continue data acquisition]]
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# [[General operation problems]]
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# [[Hardware Troubles]]
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# [[Troubles with Imaging - Troubleshooting|Troubles with Imaging]]
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# [[Troubles with Targeting]]
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# [[Troubles with Focusing and Drift Check]]
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# [[Troubles with Calibrations - Troubleshooting|Troubles with Calibrations]]
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# [[Troubles with Tomography]]
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h2. 27. [[Preferences Setup]]
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# [[Initial MSI application preference setup]]
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# [[MSI-Tomography Preferences]]
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# [[Robot MSI-Section preference set-up]]
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h2. 28. [[Node Descriptions]]
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# [[Acquisition]]
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# [[AlignZeroLoss]]
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# [[BeamFixer]]
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# [[Beam Tilt Calibrator]]
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# [[Beam Tilt Imager]]
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# [[Click Target Finder]]
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# [[Corrector]]
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# [[Dose Calibrator]]
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# [[Drift Manager]]
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# [[The EM node]]
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# [[FFT Maker]]
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# [[Focuser]]
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# [[Gon Modeler]]
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# [[Hole Finder]]
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# [[Hole Depth]]
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# [[JAHC Hole Finder (Template Hole Finder)]]
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# [[Manual Acquisition]]
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# [[Matlab Target Finder]]
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# [[Matrix Calibrator]]
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# [[Mosaic Click Target Finder]]
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# [[Mosaic Target Maker]]
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# [[Navigator]]
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# [[Phase_Plate_Aligner_Node_Class|Phase Plate Aligner]]
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# [[Pixel Size Calibrator]]
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# [[Presets Manager]]
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# [[Raster Finder]]
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# [[Raster Filter]]
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# [[RCT]]
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# [[Robot]]
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# [[RobotAtlasTargetFinder]]
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# [[Tomography]]
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# [[TEM Controller]]
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# [[Transform Manager ]]
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h2. 28. [[Create and Edit Applications]]
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# [[Use the Application Editor to create Leginon applications|Use the Application Editor in Leginon to create or edit Leginon applications]]
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# [[Edit an existing application as an xml file]]
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# [[Import Export Application Settings as json file]]
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# [[Create Leginon "Simple Application"]]
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# [["Calibrations" Application]]
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# [["MSI-Edge" Application]]
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# [["MSI-T" Application]]
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# [["MSI-raster" Application]]
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# [["MSI-Tomography" Application]]
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# [["Manual" Application]]