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Leginon Manual » History » Revision 6

Revision 5 (Amber Herold, 04/13/2010 04:29 PM) → Revision 6/137 (Amber Herold, 04/22/2010 03:46 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 Requirement 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 Leginon System]] 
     [[What is in this chapter]] 
     [[Possible Computer Set-up Configurations]] 
     [[Ports that Leginon system uses:]] 
     [[Where to Register and download Leginon system]] 
     [[Processing server-side Leginon Installation]] 
     [[Database Server-side Installation]] 
     [[Web server set up and Installation]] 
     [[Windows installation]] 
     [[Additional installation on the microscope computer:]] 
     [[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]]