Leginon Manual » History » Revision 74
Revision 73 (Anchi Cheng, 12/13/2013 07:13 PM) → Revision 74/137 (Anchi Cheng, 12/19/2013 03:50 PM)
h1. Leginon Manual {{>toc}} h2. 1. [[An introduction to Leginon]] # [[What is the Leginon System?]] # [[Terminology]] # [[Graphical User Interface]] # [[Minimum Requirements and current NRAMM setup]] # [[Getting Started]] h2. 2. [[Version Change Log]] h3. 2. 1. [[Leginon System version 2.0]] # [[pyScope Changes 2.0]] # [[New User Features 2.0]] # [[New Web Tool Features 2.0]] # [[Bug Fixes 20]] # [[Known Bugs 2.0]] h3. 2. 2. [[Leginon System version 2.1]] # [[pyScope Changes 2.1]] # [[New User Features 2.1]] # [[New Web Tool Features 2.1]] # [[Bug Fixes 2.1]] # [[Known Bugs 2.1]] h3. 2. 3. [[Leginon System version 2.2]] # [[pyScope Changes 2.2]] # [[New User Features 2.2]] h3. 2. 3. [[Leginon System version 3.0]] # [[pyScope Changes 3.0]] # [[New User Features 3.0]] h2. 3. [[Upgrade Instructions]] h3. 3. 1. [[Update within the same version using svn]] h3. 3. 2. [[Upgrade to Leginon System version 1.6|Upgrade from Previous versions to version 1.6]] h3. 3. 3. [[Upgrade to Leginon System version 2.0 from version 1.6]] # [[How to Update from v1.6 (Linux)]] # [[How to Update from v1.6 (Microscope Windows Computer)]] # [[Preparation before Using v2.x Routinely]] h3. 3. 4. [[Upgrade to Leginon System version 2.1 from version 1.6]] # [[How to Update from v1.6 (Linux)]] # [[How to Update from v1.6 (Microscope Windows Computer)]] # [[Preparation before Using v2.x Routinely]] h3. 3. 5. [[Upgrade to Leginon System version 2.1 from version 2.0]] # [[How to Update from v2.0 (Linux)]] # [[How to Update from v2.0 (Microscope Windows Computer)]] h3. 3. 6. [[Upgrade to Leginon System version 2.2 from version 2.1]] # [[How to Update from v2.1 (Linux)]] # [[How to Update from v2.1 (Microscope Windows Computer)]] # [[Check Cs value match before using Leginon after update]] h3. 3. 7. [[Upgrade to Leginon System version 3.0 from version 2.2]] # [[How to Update from v2.2 (Linux)]] # [[How to Update from v2.2 (Instrument Windows Computer)]] h3. 3. 8. [[Upgrade to Leginon System version 3.0 from version 2.2-redux]] # [[How to Update from v2.2-redux (Linux)]] # [[How to Update from v2.2 (Instrument Windows Computer)|How to Update from v2.2-redux (Instrument Windows Computer)]] h2. 4. [[Complete Installation]] # [[Four Parts of the Leginon System]] # [[What is in this Chapter]] # [[Possible Computer Set-up Configurations]] # [[Network Configuration]] # [[Download Appion Files|Where to register and download Leginon]] # [[Database Server Installation]] # [[Processing Server Installation]] # [[DD Frame Alignment Server Installation]] (only if you have a frame-saving DD camera) # [[Web Server Installation]] # [[Installation on the instrument computer|Installation on the microscope/camera Windows microscope computer]] # [[Steps involved in the installation| Steps needed for Installation Using Database Administration Tools]] # [[Add a new project for test| Create a test project for testing]] # [[Start Leginon|Perform Microscope Setup and Test run]] # [[Backup Practices]] h2. 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]] # [[Default Settings|Revert Settings]] # [[Applications]] # [[Goniometer]] h2. 6. [[Using Project Management Tools]] # [[Recommendataion-Dividing projects by long-term goal]] # [[Go to project tools page]] # [[Add a new project]] # [[Edit an existing project]] # [[Grid management]] h2. 7. [[TroubleShootInstall|Installation Troubleshooting]] # [[Getting Help]] # [[Installation/Update problems]] # [[Administration Tool problems]] # [[Test run operation problems]] # [[Network problems]] # [[Troubles with Imaging]] # [[Troubles with Calibrations]] h2. 8. [[Instrument Set-up]] # [[Calibrations required on FEI microscopes]] # [[Low dose shutter configuration for Gatan camera in Digital Micrograph program|Gatan camera configuration]] # [[Tietz camera configuration]] # [[Good Alignments Save Time]] # [[Microscope Set-up Checklist]] h2. 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]] h2. 10. [[Leginon "Manual Application"]] # [[The Application]] # [[Startup]] # [[Running "Manual" Application]] # [[Advanced Features]] # [[Using the Web viewer]] h2. 11. [[Leginon "Calibrations" Application]] # [[Importance of making calibrations]] # [[Grids for Calibration]] # [[Startup Calibrations|Startup]] # [[Creating Presets for the first time]] # [[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]] h2. 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]] # [[Optimizing Autofocus]] # [[Adding a new focus sequence to a focus node]] # [[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]] # [[Iterative Stage Movement|Iterative Stage Movement Option]] h2. 13. [[Leginon "MSI-T" Application]] # [[Summary of this application - MSI-T|Summary of this application]] # [[Creating Template]] # [[Hole Targeting Set-up for MSI-T]] # [[Exposure Targeting Set-up for MSI-T]] h2. 14. [[Leginon "MSI-Edge" Application]] # [[Summary of this application]] # [[Edge Hole Finder Set-up]] h2. 15. [[Leginon "MSI-raster" Application]] # [[Summary of this application - MSI-raster|Summary of this application]] # [[raster finder nodes set-up]] # [[Improving Autofocusing]] h2. 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]] # [[RCT calibration]] # [[RCT run protocol from a user]] h2. 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]] h2. 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]] h2. 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]] h2. 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?]] h2. 21. [[Trouble shooting]] # [[Getting Help - 2|Getting Help]] # [[Do and Do Not in leginon]] # [[Pausing and Aborting during data collection]] # [[Aborting targets that are not yet being processed]] # [[Restarting procedure to continue data acquisition]] # [[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]] h2. 22. [[Preferences Setup]] # [[Initial MSI application preference setup]] # [[MSI-Tomography Preferences]] # [[Robot MSI-Section preference set-up]] h2. 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 ]] h2. 24. [[Create and Edit Applications]] # [[Use the Application Editor to create Leginon applications|Use the Application Editor in Leginon to create or edit Leginon applications]] # [[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]]