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Leginon Manual » History » Revision 11

Revision 10 (Amber Herold, 04/22/2010 04:03 PM) → Revision 11/137 (Amber Herold, 04/22/2010 04:04 PM)

h1. Leginon Manual 

 # [[Intro|An Introduction to Leginon]] 
 # [[New1_6|Leginon System Version 1.6]] 
 # [[Update|Update to Leginon System Version 1.6]] 
 # [[CompleteInstall|Complete Installation]] 
 # [[Admin|Leginon Administration Tools]] 
 # [[Project|Using Project Management Tools]] 
 # [[TroubleShootInstall|Installation Troubleshooting]] 
 # [[EmSetup|Microscope Set-up]] 
 # [[StartLeg|Start Leginon]] 
 # [[AppManual|Leginon Manual Application]] 
 # [[AppCal|Leginon Calibrations Application]] 
 # [[AppMSI|Multi-Scale Imaging Applications in General]] 
 # [[AppMSIE|Leginon MSI-Edge Application]] 
 # [[AppMSIT|Leginon MSI-T Application]] 
 # [[AppMSIRaster|Leginon MSI-Raster Application]] 
 # [[AppMSIRCT|Leginon MSI-RCT and MSI-RCT raster Applications]] 
 # [[AppRobotScreen|Leginon Robot-MSI-Screen Applications]] 
 # [[FAQ|Frequently Asked Questions]] 
 # [[Troubleshoot|Troubleshooting]] 
 # [[AppMSIpref|Initial MSI application preference setup]] 
 # [[NodeDescribe|Node Descriptions]] 
 # [[AppCreateEdit|Create and Edit Applications]] 


 Contents 

 1. [[An introduction to Leginon]] 

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

 2. [[Leginon System version 1.6]] 

 # [[pyScope Change]] 
 # [[New User Features]] 
 # [[Updated Applications (All)]] 
 # [[New Project Web Tool Features]] 
 # [[New dbemtool Web Tool Features (1.5.1)]] 
 # [[Bug Fixes]] 
 # [[Recommended Application Preference Changes when updated from version 1.5]] 
 # [[Known Bugs]] 

 3. [[Update to Leginon System version 1.6]] 

 # [[Update from v1.1 and v1.2 NOT AVAILABLE]] 
 # [[Update from v1.3-Follow v1.4 update after performing these]] 
 # [[Update from v1.4]] 
 # [[How to Update from v1.5 (Linux)]] 
 # [[Import the new (1.6) applications included with Leginon]] 
 # [[How to Update from v1.5 (Window)]] 
 # [[Additional work at the computer controlling the microscope and camera (Window)]] 
 # [[Recommended Application Preference Changes when updated from version 1.5]] 

 4. [[Complete Installation]] 

 # [[Four Parts of the Leginon System]] 
 # [[What is in this Chapter]] chapter]] 
 # [[Possible Computer Set-up Configurations]] 
 # [[Ports used by Leginon]] that Leginon system uses:]] 
 # [[Where to register Register and download Leginon]] Leginon system]] 
 # [[Processing Server server-side Leginon Installation]] 
 # [[Database Server Server-side Installation]] 
 # [[Web Server server set up and Installation]] 
 # [[Windows Installation]] installation]] 
 # [[Additional installation on the microscope computer]] computer:]] 
 # [[Next Steps]] [[What is next]] 
 # [[Backup Practices]] 

 5. [[Leginon Administration Tools]] 

 # [[Recommandation for setup at a new institute]] 
 # [[Steps involved in the installation]] 
 # [[Set up for a new regular user]] 
 # [[More about Groups]] 
 # [[More about Instruments]] 
 # [[Applications]] 
 # [[Calibrations]] 
 # [[Goniometer]] 

 6. [[Using Project Management Tools]] 

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

 7. [[Installation Trouble shooting]] 

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

 8. [[Microscope Set-up]] 

 # [[Good Alignments Save Time]] 
 # [[Microscope Set-up Checklist]] 

 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]] 

 10. [[Leginon "Manual Application"]] 

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

 11. [[Leginon "Calibrations" Application]] 

 # [[Importance of making calibrations]] 
 # [[Grids for Calibration]] 
 # [[Startup]] 
 # [[Creating Presets for the first time]] 
 # [[Calibration without presets]] 
 # [[Pixel Size Calibration]] 
 # [[Bright and Dark reference images]] 
 # [[Image Shift matrix calibration]] 
 # [[Beam Shift matrix calibration]] 
 # [[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]] 

 12. [[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]] 
 # [[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]] 

 13. [[Leginon "MSI-Edge" Application]] 

 # [[Summary of this application]] 
 # [[Hole Targeting Set-up for MSI-Edge]] 
 # [[Exposure Targeting Set-up for MSI-Edge]] 

 14. [[Leginon "MSI-T" Application]] 

 # [[Summary of this application]] 
 # [[Creating Template]] 
 # [[JAHC finder nodes set-up]] 
 # [[Queuing Option]] 

 15. [[Leginon "MSI-raster" Application]] 

 # [[Summary of this application]] 
 # [[raster finder nodes set-up]] 
 # [[Queuing Option]] 
 # [[Improving Autofocusing]] 

 16. [[Leginon "MSI-RCT" and MSI-RCT raster" Applications]] 

 # [[Summary of these applications]] 
 # [[RCT node set-up]] 
 # [[Presets for MSI-RCT applications]] 

 17. [[Leginon "RobotMSI-Section" Application]] 

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

 18. [[Leginon "MSI-Tomography" Application]] 

 # [[Summary of this application]] 
 # [[Set-up Before Running]] 
 # [[Running the application]] 
 # [[Full Protocol on a F30 with an energy filter]] 

 19. [[Leginon "Robot-MSI-Screen" Applications]] 

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

 20. [[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?]] 

 21. [[Trouble shooting]] 

 # [[Getting Help]] 
 # [[Do and Do Not in leginon]] 
 # [[Pausing and Aborting during data collection]] 
 # [[General operation problems]] 
 # [[Hardware Troubles]] 
 # [[Troubles with Imaging]] 
 # [[Troubles with Targeting]] 
 # [[Troubles with Focusing and Drift Check]] 
 # [[Troubles with Calibrations]] 
 # [[Troubles with Tomography]] 

 22. [[Initial MSI application preference setup]] 

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

 23. [[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 ]] 

 24. [[Create and Edit Applications]] 

 # [[Use the Application Editor to create Leginon applications]] 
 # [[Reload and Edit an existing application]] 
 # [[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]]