Leginon Manual¶

1. An Introduction to Leginon
2. Leginon System Version 1.6
3. Update to Leginon System Version 1.6
4. Complete Installation
5. Leginon Administration Tools
6. Using Project Management Tools
7. Installation Troubleshooting
8. Microscope Set-up
9. Start Leginon
10. Leginon Manual Application
11. Leginon Calibrations Application
12. Multi-Scale Imaging Applications in General
13. Leginon MSI-Edge Application
14. Leginon MSI-T Application
15. Leginon MSI-Raster Application
16. Leginon MSI-RCT and MSI-RCT raster Applications
17. Leginon Robot-MSI-Screen Applications
18. Frequently Asked Questions
19. Troubleshooting
20. Initial MSI application preference setup
21. Node Descriptions
22. 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]]