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Index by title

• Acquisitionpy
• Add a new project shared
• Add host
• Alternative reduxd installation on file server
• Authors
• Bug Fixes 21
• Bug Fixes 30
• CAMC ini setup
• Comtypes installer
• Configure leginoncfg 2 1
• Configure sinedoncfg 2 1
• Creating a new Leginon node
• DE-12 Installation Pyscope Test
• Download Appion and Leginon Files
• EM Workshop - Leginon Users Group
• Eucentric focus
• Extra supporting package table
• Faraday Cup Measurment Notes
• Forum conversion
• Gatan K2 Instruments cfg
• Gatan K2 Support Update of trunk from before 17514 to higher than 17561
• Grid management shared
• How to Update from v22-redux (Linux)
• Installation on the microscope computer 21
• Installing comtypes
• Install Leginon-only Packages
• Install SSH module for PHP webserver
• Instrumentcfg for DE-12
• Instrumentscfg for 21
• Instrumentscfg for 22
• Instrumentscfg for 30
• Instrumentscfg for falcon orius
• JEOL setup
• Krios1-K2-NYSBC-large shift
• Leginon Brainstorm
• Leginon Developer Guide
  • Fake calibrations for Leginon simulator
  • Numextension
  • Premade Realistic-looking calibration and images for simulation
  • Setup simulator with VMware
• Leginon Homepage
  • Leginon Manual
    • Administration Tools
      • Applications
      • Calibrations
      • Default Settings
      • Goniometer
      • More about Groups
      • More about User Tools
      • Recommandation for setup at a new institute
      • Set up for a new regular user
      • Steps involved in the installation
    • An Introduction to Leginon
      • Getting Started
        • Getting Started as a basic Leginon user
        • Getting Started as a basic Leginon user in docbook version
        • Getting Started as a Super User
        • Getting Started as a System Administrator
      • Graphical User Interface
      • Minimum Requirements and current NRAMM setup
        • Buffer(Ingestion) Server setup
        • Compatible Instrument
        • Current NRAMM setup
          • NRAMM buffer server hardware
        • Minimum Requirements for frame-saving direct detectors
        • Minimum Requirements for non-frame-saving camera
        • NCCAT Hardware
        • SEMC file storage policy
      • Supported Instrument
        • JEOL 1230 installation specifics
      • Terminology
      • What is the Leginon System
    • Camera length calibration
    • Complete Installation
      • Additional Database Server Setup after Web Server Installation
      • Autoinstaller for CentOS
      • Backup Practices
      • Database Server Installation
      • Database Server Setup to allow connection from the instruments
      • DD Frame Alignment Server Installation
      • File Server Setup Considerations
      • Four Parts of the Leginon System
      • Installation on the instrument computers
        • Installation on the camera computer
          • Ceta camera support
          • Direct Electron DE-12 direct detection device support
            • Acquiring summed frame image thru Leginon
            • Adding DE-12 to Leginon
            • DDD raw frame file transfer
            • DE-12 introduction
            • DE raw frame saving
            • Make DE movie stack
            • Using DE DDD in Leginon
          • Eagle camera installation and setup
          • Falcon-Orius Combination Installation Notes
          • Falcon 3 support
          • Falcon camera support
            • Falcon acquire image
            • Falcon gain correction
              • Falcon raw frame saving configuration xml
            • Falcon Orius combo installation and setup
              • Comtypes installation
            • Falcon raw frame saving
            • Leginon settings modification for Falcon camera
            • Using Falcon Orius combo in Leginon
          • Gatan K2 Summit Support
            • Gatan K2 installation and setup
              • Install SerialEM DigitalMicrograph plugin
              • Older k2 dmsem configuration
              • Semccd installation
            • Gatan K2 Installation Notes
            • Gatan K2 Installation Pyscope Test
              • Pyscope test k2 save frames
            • K2 calibration
            • K2 Summit introduction
            • Make DDD movie stack
              • Make movie stack with darkbrightnormgain references yourself without LeginonAppion libraries
            • Using Gatan K2 Summit in Leginon
              • K2 acquire image
              • K2 camera sensitivity
              • K2 gain correction
              • K2 raw frame saving
          • Gatan K3 installation and setup
            • Gatan K3 Installation Pyscope Test
            • Gatan K3 Instrumentscfg
          • Gatan on Windows-32
            • Gatan on Windows-32 with TecnaiCCDdll
            • Gatan on Windows with semccddll
              • Dm camera configuration
              • Gatan UltraScan dmsem Installation Pyscope Test
                • Pyscope test result array
          • Instrumentcfg setup on FEI scope where K2 fakes another camera in order to control the shutter
          • Tietz camera installation and setup
          • Tietz camera installation and setup using EM-MENU
        • Installation on the microscope computer 30
          • FEI Talos installation specifics
          • FEI TecnaiTitan installation specifics
            • Setup feicfg
            • Unable to initializ Tecnai interface error
              • Find and register a dll file as command components in Windows
          • JEOLCOM installation specifics
            • JEOL External3 setup
            • Leginon Operation for JEM scopes
            • Setup and Calibration for jeolcfg
              • J2100f k2 preset design
              • J3200 de20 preset design
        • Trouble shooting with Python IDLE
        • Windows General Package Requirement
          • Git for windows cloning
          • Git for windows installation
          • Windows myami svn checkout
        • Windows Installation All
          • Set pythonpath environment variable for local myami sandbox
        • Windows Myami Configuration
        • Windows Package Requirement 30
        • Windows Setup After Software Installation
      • Installation on the microscope computer
        • Auoit program script compilation
      • Network Configuration
        • An example of working port-forwarding configuration
        • Ports used by Leginon
      • Next Steps
      • Possible Computer Set-up Configurations
      • Processing Server Installation
        • Compile Ace2
        • Compile FindEM
        • Compile Radermacher
        • Configure leginoncfg
        • Configure sinedoncfg
        • Create simulated instrumentscfg
        • Download Leginon Files
        • Explanation of Sample Names
        • Install External Packages
        • Install Leginon Packages
        • Install supporting packages
        • Install Xmipp
        • Perform system check
        • Test Appion
      • Select Linux distribution to use
        • Instructions for installing CentOS on your computer
      • Web Server Installation
        • Check php information
          • Start NFS
        • Configure Operating System
        • Configure phpini
        • Differences between Linux flavors
        • Install Apache Web Server
        • Install phpMyAdmin
        • Install Redux image server
        • Install the MRC PHP Extension
        • Install the Web Interface
          • Install the Web Interface Advanced
        • Install Web Server Prerequisites
        • Potential Problems
      • What is in this Chapter
      • Where to register and download Leginon
      • Windows Installation
    • Create and Edit Applications
      • "Calibrations" Application
      • "Manual" Application
      • "MSI-Edge" Application
      • "MSI-raster" Application
      • "MSI-T" Application
      • "MSI-Tomography" Application
      • Create Leginon "Simple Application"
      • Edit an existing application as an xml file
      • Import Export Application Settings as json file
      • Reload and Edit an existing application
      • Use the Application Editor to create Leginon applications
    • Database migrating exportimport scripts
    • Data Collection Setup Examples
      • 19 Å mouse mFth1 recombinant apoferritin image-shift data collection with image-shift aberration-correction
      • Sub-3Å proteasome stage-shift data collection
        • Krios-K2-TSRI Presets
    • Frequent Asked Questions
      • How does Leginon Name the Files
      • What is the definition of ice thickness in the hole finders
      • Why does the first Grid Image Not Numbered 00001
    • How to Update from v32 (Instrument Windows Computer)
      • Tecnai to fei Instrumentscfg change
    • How to Update from v34 (Linux)
      • How to Update from v34 (Instrument Windows Computer)
    • How to Update from v35 (Instrument Windows Computer)
    • How to Update from v35 (Linux)
    • Installation Troubleshooting
      • Administration Tool problems
      • Getting Help
      • InstallationUpdate problems
      • Network problems
      • Test run operation problems
      • Troubles with Calibrations
      • Troubles with Imaging
    • Instrument Set-up
      • Calibrations required on FEI microscopes
        • HM Beam Shift Image Shift Calibration
        • TEM Scripting Beam Tilt Calibration
          • Running get beamtiltscalepy
      • Calibrations required on the microscope alone before starting Leginon
        • Calibration required on JEOL
      • Good Alignments Save Time
      • Leginon image orientation
      • Low dose shutter configuration for Gatan camera in Digital Micrograph program
      • Microscope Set-up Checklist
      • Tietz camera configuration
    • Instrument Usage Specifics
      • Instrument Selection
        • Camera Configuration
          • Saving frames from direct detectors
    • Lacey Carbon Application
      • RasterFC Finder node set-up
      • RasterFC Lacey carbon rastering
        • Creating the Application from existing MSI-Raster Application
      • Using MSI-T application to collect Lacey Carbon support data
    • Leginon "Calibrations" Application
      • Apply Extra rotation
      • Autofocus Calibration with Beam Tilt Node
      • Beam Shift matrix calibration
      • Beam Size Calibration
      • Bright and Dark reference images
        • Using image shift matrix calibration to refine image shift scale in jeolcfg
      • Calibration without presets
      • Checking Matrix and Modeled Stage Position Calibration
        • Test stage position targeting reproducibility
      • Check Phase Plate Patches
        • Generate Phase Plate Condition Map
        • Inspect the phase plate slot at low magnification
      • Creating Presets for the first time
      • Dose (Camera Sensitivity) Calibration
      • Efficient way to calibrate matrixes for all mags in the same projection mode
      • Grids for Calibration
      • Image Beam Compensation Calibration
      • Image Shift matrix calibration
        • Refine IMAGE SHIFT SCALE in jeolcfg
      • Importance of making calibrations
      • Lens Aberration Correction Calibration for Beam-Image Shift Targeting
        • Download beam-image shift values for Relion 3 beam-tilt refinement
        • Using Leginon manual tools to calibrate beam-image shift aberration correction
        • Using TFS AutoCTF to calibrate beam-image shift aberration correction
      • Modeled Stage Position calibration
      • Pixel Size Calibration
      • Stage Position matrix calibration
        • Scaling Stage Position Matrix
      • Startup Calibrations
    • Leginon "Manual Application"
      • Advanced Features
      • Running "Manual" Application
      • Startup
      • The Application
      • Using the Web viewer
        • 2 Way Viewer
        • 3 Way Viewer
        • Common Features
        • Dual Viewer
        • Image Tools
        • Image Viewer
    • Leginon "MSI-Edge" Application
      • Edge Hole Finder Set-up
      • Exposure Targeting Set-up for MSI-Edge
      • Hole Targeting Set-up for MSI-Edge
      • Summary of this application
    • Leginon "MSI-raster" Application
      • Improving Autofocusing
      • Queuing Option - MSI-raster
      • Raster finder nodes set-up
      • Summary of this application - MSI-raster
    • Leginon "MSI-RCT" and MSI-RCT raster" Applications
      • Best grids for RCT
      • Presets for MSI-RCT applications
      • RCT calibration
      • RCT node set-up
      • RCT run protocol from a user
      • Summary of this application - MSI-RCT
        • Good negative stained images for RCT
    • Leginon "MSI-T" Application
      • Creating Hole Template
      • Exposure Targeting Set-up for MSI-T
      • Exposure Targeting Set-up for MSI-T for Four holes
        • New Exposure Targeting Set-up in MSI-T for Multiple holes
      • Hole Targeting Set-up for MSI-T
      • Queuing Option - MSI-T
      • Summary of this application - MSI-T
    • Leginon "MSI-T-Tilt" Application
      • MSI-T-Tilt Installation
      • MSI-T-Tilt Operation
      • Summary of this application - MSI-T-Tilt
    • Leginon "MSI-Tomography" Application
      • Fitting the tilt axis model
      • Full Protocol on a F30 with an energy filter
      • Reading the tomography graphs
      • Running the application
      • Set-up Before Running
      • Summary of this application - MSI-Tomo
      • Using "MSI-SimuTomography" Application for debugging
    • Leginon "Robot-MSI-Screen" Applications
      • 1st Pass application
      • 2nd Pass application
      • Evaluation application
      • Operation
      • Robot node set-up
      • Summary of this application - Robot-MSI-Screen
      • Upload Grids
    • Leginon "RobotMSI-Section" Application
      • Other special preference set-up
      • Raster Generation node set-up
      • Summary of this application - RobotMSI
      • Tips on Operation
    • Leginon System version 31
      • New User Features 31
        • Child Imaging Area and Beam Diameter Display in TargetFinder Nodes
      • Pyscope Changes 31
    • Leginon System version 32
      • New User Features 32
      • Pyscope Changes 32
        • JEOL scope support
    • Leginon System version 33
      • New User Features 33
        • How often should the phase plate moved to the next patch
        • Ice Thickness Measurement using Energy Filter
          • Introduction and description of method
          • Notes on Use
          • Parameters needed
        • MSI-PP Appplication
        • Slack notification for Leginon errors
          • Activate Slack notifications in Leginon
        • Special Beam Tilt Calibration for Phase Plate
        • Volta Phase Plate Usage
          • Phase Plate Aligner Node Class
            • Phase Plate Aligner Tool Bar
          • Volta Phase Plate Control Installation Reguirements
      • PyScope Changes 33
    • Leginon System version 34
    • Leginon System version 35
    • Leginon System version 36
      • Pyscope Changes 36
      • Sinedon Changes 36
    • Leginon System version 37
      • New User Features 37
    • Leginon System version pymysql
      • Install pymysql on Windows PC
    • Multi-Scale Imaging Applications in General
      • Adding a new focus sequence to a focus node
      • Fix beam shift during data collection
      • Flavors of MSI applications
      • Initial MSI application preferences
      • Iterative Stage Movement
        • Determine Target Tolerance and Acceptable Tolerance
      • Monitor Progress of Queued Targets
      • MSI Operation
        • Setup Auto Square Finder using example targets
      • MSI Quick-start
      • MSI set up in more details
      • Multi-Scale Imaging Concept
      • Optimizing Autofocus
      • Pre-MSI Set-up
        • EF-TEM Krios-K2-Ceta Presets
      • Queuing Example 1 - Exposure Targeting
      • Queuing Example 2 - Hole Targeting only
      • Queuing Example 3 - Both Exposure and Hole Targeting
      • Queuing option
      • Special Operation Preference setup
      • Special Operation setup
      • Summary of MSI applications
      • Ways of Moving to Targets in Nodes that acquire images inside MSI
        • Image Beam Shift matrix calibration
    • New User Features 34
      • Auto hole finding for stitched square
      • Black Stripe Detection
      • Falcon III integration
      • Full support of K2K3 LZW compressed tiff file saving and processing
      • K3 integration
      • Tomography dose symmetrical tilt scheme
    • New User Features 35
      • Aperture selection through tem controller
      • Continuous tilt electron diffraction recording
        • AutoIt program and script compilation
        • Setup Ceta to use Advanced TEM Scripting
        • Setup df preset
        • Setup Diffraction mode TEM instrument
        • Setup movie upload with diffrtransferpy
        • TIA raw data conversion
        • MSI-Diffr application
      • K3 fast return with 8x8 statistic image
      • Tivips f416 electron diffraction recording
        • Create Leginon view port
    • New User Features 36
      • Appion autoRelauncher
      • Falcon 4 EER integration
        • Import falcon4 gain reference from TFS program
        • Setup falcon4 eer
      • Multi-grid autoscreening
        • Check list for each autoscreening run
        • First-time autoscreening setup
          • Settings for Target Sampling
          • Setup Ptolemy CLI for exposure targeting
          • Setup Ptolemy CLI shell script
        • MSI-Ptolemy API information for developers
        • MSI-Ptolemy application
        • Ptolemy installation and setup
        • Run autoscreenpy
        • Trouble shooting Ptolemy hole finding
      • Tilt-wrangler launcher in appion
    • Node Descriptions
      • Acquisition
      • AlignZeroLoss
      • BeamFixer
      • Beam Tilt Calibrator
      • Beam Tilt Imager
      • Click Target Finder
      • Corrector
      • Dose Calibrator
      • Drift Manager
      • FFT Maker
      • Focuser
      • Gon Modeler
      • Hole Depth
      • Hole Finder
      • JAHC Hole Finder (Template Hole Finder)
      • Manual Acquisition
      • Matlab Target Finder
      • Matrix Calibrator
      • Mosaic Click Target Finder
      • Navigator
      • Pixel Size Calibrator
      • Presets Manager
      • Raster Filter
      • Raster Finder
      • RCT
      • Robot
      • RobotAtlasTargetFinder
      • TEM Controller
      • The EM node
      • Tomography
      • Transform Manager
    • Preferences Setup
      • Initial MSI application preference setup
      • Krios Leginon Preferences
      • MSI-Tomography Preferences
        • Set up dose parameters in Tomography
      • Robot MSI-Section preference set-up
    • PyScope Changes 34
    • PyScope Changes 35
      • Direct assignment of frame fliprotation in dmsemcfg for Gatan K2 and K3 cameras
      • Falcon 4 support
      • Hitachi 7800 support
        • Hitachi install
          • Setup and Calibration for hhtcfg and focus offset
        • Hitachi setup
        • Leginon Operation for HT7800
    • Start Leginon
      • Run Leginon Client on the Instrument Computers
      • Start Leginon at your main working station remotely
      • Start leginon what is next
      • Test Leginon on the Computer Controlling the Microscope
      • Test Leginon with Simulator
      • Test Network Connection Between Remote and Instrument Computers
        • Configure pyamicfg for host-ip pairings
        • Reorder the network connections
    • Trouble shooting
      • Aborting targets that are not yet being processed
      • Do and Do Not in leginon
      • General operation problems
      • Getting Help - 2
      • Hardware Troubles
      • Load mysqldumped databases
      • Mysqldump of your database
      • Pausing and Aborting during data collection
      • Restarting procedure to continue data acquisition
      • Troubles with Calibrations - Troubleshooting
      • Troubles with Focusing and Drift Check
      • Troubles with Imaging - Troubleshooting
      • Troubles with Targeting
      • Troubles with Tomography
    • Upgrade Instructions
      • How to Update from v22 (Instrument Windows Computer)
      • PyScope Changes 21
      • Update within the same version using git
      • Update within the same version using svn
      • Upgrade to Leginon System trunk version from version 22
      • Upgrade to Leginon System version 16
        • Additional work at the computer controlling the microscope and camera (Window)
        • How to Update from v15 (Linux)
        • How to Update from v15 (Window)
        • Import the new (16) applications included with Leginon
        • Recommended Application Preference Changes when updated from version 15 update
        • Update from v11 and v12 NOT AVAILABLE
        • Update from v13-Follow v14 update after performing these
        • Update from v14
      • Upgrade to Leginon System version 21 from version 16
      • Upgrade to Leginon System version 21 from version 20
        • How to Update from v20 (Linux)
        • How to Update from v20 (Microscope Windows Computer)
      • Upgrade to Leginon System version 22 from version 21
        • Check Cs value match before using Leginon after update
        • How to Update from v21 (Linux)
        • How to Update from v21 (Microscope Windows Computer)
      • Upgrade to Leginon System version 2x from version 16
        • How to Update from v16 (Linux)
        • How to Update from v16 (Microscope Windows Computer)
        • Preparation before Using v2x Routinely
      • Upgrade to Leginon System version 30 from version 22
        • How to Update from v22 (Linux)
    • Upgrade to Leginon System version 31 from version 30
      • How to Update from v30 (Instrument Windows Computer)
      • How to Update from v30 (Linux)
    • Upgrade to Leginon System version 32 from version 31
      • How to Update from v31 (Linux)
        • How to Update from v31 (Instrument Windows Computer)
    • Upgrade to Leginon System version 33 from version 32
      • How to Update from v32 (Linux)
    • Upgrade to Leginon System version 34 from version 33
      • How to Update from v33 (Instrument Windows Computer)
      • How to Update from v33 (Linux)
    • Upgrade to Leginon System version 35 from version 34
    • Upgrade to Leginon System version 36 from version 35
    • Using FEI Titan Krios in Leginon
      • Auto Nitrogen Filler Triggering
    • Using Project Management Tools
      • Add a new project
      • Add a new project for test
      • Edit an existing project
      • Go to project tools page
      • Grid management
      • Installation
      • Recommendataion-Dividing projects by long-term goal
      • Share an experiment session with a non-owner user
    • Version Change Log
      • Leginon System version 1 6
        • Bug Fixes
        • Known Bugs
        • New dbemtool Web Tool Features (151)
        • New Project Web Tool Features
        • New User Features
        • PyScope Change
        • Recommended Application Preference Changes when updated from version 15
        • Updated Applications (All)
      • Leginon System version 20
        • Bug Fixes 20
        • Known Bugs 20
        • New User Features 20
        • New Web Tool Features 20
        • PyScope Changes 20
      • Leginon System version 21
        • Known Bugs 21
        • New User Features 21
        • New Web Tool Features 21
      • Leginon System version 22
        • New User Features 22
  • Leginon System version beta
    • New User Features beta
    • Pyscope Changes beta
  • Sub-3Å proteasome image-shift data collection
    • Krios1-K2-NYSBC
    • Scaling Stage Position Matrix Calibration
  • Using Leginon at Scripps
• Leginon System version 30
  • New User Features 30
  • Pyscope Changes 30
• Link to ubuntu
• Linux distribution recommendation
• Locate global config directory on Windows
• Manual Focusing Tool
• More about Groups shared
• Mosaic Target Maker
• MSI Quick-start for DD only
• Packages installed by pysetupsh
• PyScope Changes 22
• Recommandation for setup at a new institute shared
• Redux
  • Using Redux to serve images on myamiweb
    • Start redux with systemd
• Reference session
• Reload atlas
• Revert Settings
• Set up for a new regular user shared
• Special Instructions for FEI Eagle Camera
• Steps involved in the installation shared
• Strange dimension cameras
• Testing auto-installation
• Testing pyscope instrument
• Tietz camera trouble shoot
• Trouble shooting semccd socket connection
• Upgrade to Leginon System version 30 from version 22-redux
• Using imcache to cache mrc images as jpeg images of the default size on myamiweb
• Using Leginon on a system where the microscope and camera are controlled by different computers
• Windows 32 External Package Installers Common
• Windows Camera Package Requirement
  • Protobuf installation instruction
  • SerialEM SEMCCD-GMS plugins
• Windows External Package installers
  • Windows 32 External Package Installers
• Windows Microscope Package Requirement
• Windows Myami Package installers

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