Leginon Manual » History » Revision 13
Revision 12 (Amber Herold, 04/22/2010 04:05 PM) → Revision 13/137 (Amber Herold, 04/22/2010 04:47 PM)
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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]] # [[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]] 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. [[TroubleShootInstall|Installation Troubleshooting]] # [[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 Calibrations|Startup]] [[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]]