Leginon Manual » History » Revision 6
Revision 5 (Amber Herold, 04/13/2010 04:29 PM) → Revision 6/137 (Amber Herold, 04/22/2010 03:46 PM)
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]]