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 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]]