Leginon Manual » History » Revision 7
Revision 6 (Amber Herold, 04/22/2010 03:46 PM) → Revision 7/137 (Amber Herold, 04/22/2010 03:47 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 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]]