Leginon

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]]

# [[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]]

# [[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 - MSI-T|Summary of this application]]

# [[Creating Template]]

# [[JAHC finder nodes set-up]]

# [[Queuing Option - MSI-T|Queuing Option]]

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]]

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]]

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]]

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]]

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]]

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 - Troubleshooting|Troubles with Imaging]]

# [[Troubles with Targeting]]

# [[Troubles with Focusing and Drift Check]]

# [[Troubles with Calibrations - Troubleshooting|Troubles with Calibrations]]

# [[Troubles with Tomography]]

22. Preferences Setup 

# [[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]]