Leginon Manual » History » Revision 30
Revision 29 (Amber Herold, 04/23/2010 02:38 PM) → Revision 30/137 (Anchi Cheng, 05/06/2010 04:06 PM)
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]]
h2. 2. 1. [[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]]
h2. 2. 2. [[Leginon System version 2.0]]
# [[pyScope Change 2.0]]
# [[New User Features 2.0]]
# [[New Web Tool Features 2.0]]
# [[Bug Fixes2.0]]
# [[Known Bugs 2.0]]
h2. 3. [[Upgrade Instructions]]
h2. 3. 1. [[Upgrade [[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]]
h2. 3. 2. [[Upgrade to Leginon System version 2.0 from version 1.6]]
# [[How to Update from v1.6 (Linux)]]
# [[How to Update from v1.6 (Window)]]
# [[Additional work at the computer controlling the microscope and camera (Window) from v1.6]]
h2. 4. [[Complete Installation]]
# [[Four Parts of the Leginon System]]
# [[What is in this Chapter]]
# [[Possible Computer Set-up Configurations]]
# [[Ports used by Leginon]]
# [[Where to register and download Leginon]]
# [[Processing Server Installation]]
# [[Database Server Installation]]
# [[Web Server Installation]]
# [[Windows Installation]]
# [[Additional installation on the microscope computer]]
# [[Next Steps]]
# [[Backup Practices]]
h2. 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]]
h2. 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]]
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. [[Microscope Set-up]]
# [[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. [[Leginon "Calibrations" Application]]
# [[Importance of making calibrations]]
# [[Grids for Calibration]]
# [[Startup Calibrations|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]]
h2. 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]]
h2. 13. [[Leginon "MSI-Edge" Application]]
# [[Summary of this application]]
# [[Hole Targeting Set-up for MSI-Edge]]
# [[Exposure Targeting Set-up for MSI-Edge]]
h2. 14. [[Leginon "MSI-T" Application]]
# [[Summary of this application - MSI-T|Summary of this application]]
# [[Creating Template]]
# [[JAHC finder nodes set-up]]
# [[Queuing Option - MSI-T|Queuing Option]]
h2. 15. [[Leginon "MSI-raster" Application]]
# [[Summary of this application - MSI-raster|Summary of this application]]
# [[raster finder nodes set-up]]
# [[Queuing Option - MSI-raster|Queuing Option]]
# [[Improving Autofocusing]]
h2. 16. [[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]]
h2. 17. [[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. 18. [[Leginon "MSI-Tomography" Application]]
# [[Summary of this application - MSI-Tomo|Summary of this application]]
# [[Set-up Before Running]]
# [[Running the application]]
# [[Full Protocol on a F30 with an energy filter]]
h2. 19. [[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. 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?]]
h2. 21. [[Trouble shooting]]
# [[Getting Help - 2|Getting Help]]
# [[Do and Do Not in leginon]]
# [[Pausing and Aborting during data collection]]
# [[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. 22. [[Preferences Setup]]
# [[Initial MSI application preference setup]]
# [[MSI-Tomography Preferences]]
# [[Robot MSI-Section preference set-up]]
h2. 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 ]]
h2. 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]]