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Myami Documentation
An Introduction to Leginon
Initializing search
    leginon-org/leginon
    • Appion
    • Leginon
    leginon-org/leginon
    • Appion
        • Appion Manual
          • An Introduction to Appion
          • Authors
          • What is Appion
          • Appion User Guide
          • Administration Tools Guide
            • Appion Processing
              • Ab Initio Reconstruction
              • EMAN Common Lines
              • IMAGIC Angular Reconstitution
              • OTR Volume
              • RCT Volume
              • CTF Estimation
              • Ace 2 Estimation
                • Ace Estimation
                • Ace script
                • Aceman
              • CtfFind Estimation
              • Phase plate CTF Estimation
              • Common Workflow
              • Quality Assessment
              • Random-Conical Tilt (RCT) Reconstruction workflow
              • Step by Step Guide
              • Trimer processing workflow
            • CryoSPARC
              • Direct Detector Frame Processing
              • Catch up DD frame alignment
              • GainDark correction of the raw frame with or without drift correction
            • IMAGIC Multi Reference Alignment
              • Image Assessment
              • Multi Img Assessment
              • Run Image Rejector
              • Web Img Assessment
              • Import Tools
              • EMDB to Model
              • PDB to Model
              • PDB tp Model
              • Upload Model
                • Upload More Images
                • Upload image grouping
              • Upload Particles
              • Upload Stack
              • Upload Template
              • Particle Alignment
                • Run Alignment
                • Ed's Iteration Alignment
                • Spider Reference-based Alignment
                • Spider Reference-free Alignment
                • Xmipp Maximum Likelihood Alignment
                • Xmipp Reference-based Maximum Likelihood Alignment
                • Run Feature Analysis
                • Spider Coran Classification
                • Xmipp Kerden Self-Organizing Map
                • Xmipp Rotational Kerden Self-Organizing Map
                • Run Particle Clustering
                • Hierarchical or K-means Clustering
              • Particle Selection
              • Dog Picking
              • Manual Picking
                • Random Conical Tilt Picking
                • Align and Edit Tilt Pairs
                • Auto Align Tilt Pairs
              • Template Picking
            • Processing Cluster Login
              • Refine Reconstruction
              • EMAN Refinement
              • Frealign Refinement
              • IMAGIC Refinement
              • Refinement Post-processing Procedures
              • SPIDER Refinement
              • Region Mask Creation
              • Crud Finding
              • Manual Masking
              • Maskiton
            • Repeat from other session
              • Stacks
                • More Stack Tools
                • Combine Stacks
                • Convert Stack into Particle Picks
                • Jumpers SubStack
                  • View Stacks
                  • Center Particles
                  • Create Substack
                  • Filter by MeanStdev
                  • Sort Junk
              • Stack Creation
              • Synthetic Data
              • Synthetic Dataset Creation
            • Terminology
              • Tomography
              • Align Tilt-Series
              • Align tilt series
              • Create full tomogram
                • Create tomogram subvolume
                • Average tomogram subvolumes
              • Upload full tomogram
            • Upload Refinement
            • Xmipp 3 Clustering 2D Alignment
            • Appion and Leginon Database Tools
              • Administration
              • Applications
              • Goniometer
              • Groups
              • Instruments
              • Revert Settings
              • Users
            • Hole Template Viewer
              • Image Viewers
              • 2 Way Viewer
              • 3 Way Viewer
              • Common Features
              • Dual Viewer
              • Image Viewer
              • RCT viewer
            • LOI - Leginon Observer Interface
              • Project DB
              • Create New Project
              • Create a Project Processing Database
              • Edit Project Description
              • Edit Project Owners
              • Grid Management
              • Share a Project Session with another User
              • Unlink a Project Processing Database
                • Upload Images to a new Project Session
                • Image pair upload for rct
              • View Projects
              • View a Summary of a Project Session
            • Tomography Tool
              • User Management
              • Enable User Authentication
              • Logout
              • Modify Your Profile
              • New User Registration
              • Retrieve Forgotten Password
          • Appion output
          • Complete Installation
          • Additional Database Server Setup after Web Server Installation
          • Changes to auto-installed appion for production usage
            • Create a Test Project
            • Create a Processing Database
            • Process Images
          • Database Server Installation
          • Download additional Software (CentOS Specific)
          • File Server Setup Considerations
          • Install using the auto-installation tool
          • Installation Troublshooting Guide
          • Installing Appion with an existing Leginon installation
          • Instructions for installing CentOS on your computer
          • Instructions for installing Fedora on your computer
            • Processing Server Installation
              • Compile FindEM
              • Install FindEM from source
            • Compile Radermacher
            • Configure appioncfg
            • Configure leginoncfg
            • Configure sinedoncfg
            • Download Appion Files
            • Explanation of Sample Names
              • Install Ace2
              • Compile Ace2 from source
            • Install Appion Packages
            • Install EMAN
            • Install EM Hole Finder
              • Install External Packages
              • Install MotionCor2
            • Install Imod
            • Install Protomo
            • Install Protomo2
            • Install SIMPLE
            • Install SPIDER
            • Install UCSF Chimera
            • Install Xmipp
              • Install dosefgpu driftcorr
              • Install motioncor2 shared
            • Install supporting packages
            • Perform system check
            • Test Appion
          • Security Considerations
          • Select Linux distribution to use
            • Setup Remote Processing
            • ClusterPhpSettings
            • Configure web server to submit job to local cluster
            • Configure web server to submit jobs
            • Install SSH module for PHP
            • Setup job submission server
            • Testing job submission
            • Web Server Installation
            • Check php information
            • Configure Operating System
            • Configure phpini
            • Differences between Linux flavors
            • Download Appion and Leginon Files
            • Install Apache Web Server
            • Install Redux image server
            • Install SSH module for PHP webserver
            • Install Web Server Prerequisites
            • Install phpMyAdmin
              • Install the MRC PHP Extension
              • Troubleshooting Notes
              • Install the Web Interface
              • Install the Web Interface Advanced
            • Potential Problems
            • Start NFS
          • Upgrade Instructions
          • Minor release update
          • Upgrade From 20x
          • Upgrade From 21x
          • Upgrade From 22-redux
          • Upgrade From 22x
            • Upgrade From 30 or above
            • New support package requirement for 33
          • Version Change Log
          • Version 32 Change Log
        • Developers guide
          • AMI Eclipse Quick Start Guide
          • Example config file
        • Adding refine python parts
        • Adding refine runjob
        • Appion Testing
        • Appion tricks
        • CSS notes
        • Cluster job overview
          • Coding Best Practices
            • Code Review Guide
            • Code development process
            • Purpose of Code Reviews
        • Common variables used
        • Error Handling
        • General Best Practices
        • Git
        • How to add a launch page
        • How to add a new refinement method
        • How to add an AppionLoop GUI page
        • How to test upload images with your own sandbox
        • Javascript notes
          • MySQL Notes
          • Mysql Nested Subqueries Problem
        • Myami code diagram
        • Object Oriented Programming
        • PHP notes
        • Python notes
        • Refine Refactor documentation
        • Setup Local Databases
        • Subversion
        • Test datasets at AMI
        • Useful shell commands
        • Using basicReportinc
          • EMG Redmine Quick Start Guide
          • Issue Workflow Tutorial
          • Wiki Tips
          • Install Appion and Leginon using the auto installation tool share
          • Reconfigure the database
          • Regkey request
          • Processing Server External Packages Installation
          • External Package requirement of Appion scripts
            • Package executable alias name in Appion
            • Package alias table
          • CentOS6 installation
            • Install Free Hand Test
            • FreeHand compile
          • Download Appion Files Shared
          • Currrent myami release
          • Install supporting packages Shared
          • Extra supporting package table
          • Linux distribution recommendation
          • Link to ubuntu
          • Web Server Installation on CentOS 6
          • Current myami release checkout
          • 2010 Appion Developer Workshop
          • 2010 ADWAdd a new option to a program
          • 2010 ADWCreate an alignment program from scratch
          • 2010 ADWOrganization of the PHP programs
          • 2010 ADWOrganization of the Python programs
          • 2010 ADWCreate an image uploader program from scratch
        • 2 Way Viewer Shared
        • Alignment SubStacks
        • Appion CTF parameter definition
        • Appion citations
        • Appion config advanced
        • Appion forum
        • Brignole et al 2009
        • Centos installation shared
        • Code Standards
        • Configure appioncfg shared
        • Configure leginoncfg 2 1
        • Configure leginoncfg Shared
        • Configure sinedoncfg 2 1
        • Configure sinedoncfg shared
        • Convert Mass into Volume
        • Create Appion Session
        • DB Migration Process
        • Database Server Installation Shared
        • Database Setup After Webserver initialization Shared
        • Default groups
        • Default users
        • Doc test notes
        • Download additional Software (Fedora Specific)
        • File Formats
        • File Server Setup Considerations Shared
        • HTML notes
        • Helical Image Processing
        • Helical Image Processing (PHOELIX)
        • Helical Processing
        • How to run manual picking and mask making
        • Image Viewers Shared
        • Index of test scripts
        • Install Appion Packages Shared
        • Install Appion Packages Short Shared
        • Install Appion bin shared
        • Install EMAN2
        • Install EPEL shared
        • Install Grigorieff lab software
        • Install SSH module for PHP shared
        • Install Torque
        • Install Torque Client
        • Install dosefgpu driftcorr shared
        • Install myami-22 on guppy
        • Install phpMyAdmin shared
        • Job submission vs direct Appion Script running from terminal
        • Make a New Stack
        • Mount NFS on a Mac
        • Myami on Ubuntu
        • New support package requirement for 32
        • Notes from Recon meeting
        • Perform System Check Shared
        • Potential job submission problems
        • Processing Server Installation Shared
        • Python Coding Standards
        • Reconstruction Parameters
        • Refinement Package Status
        • Run Database Update Script
        • Start redux with systemd
        • Start with existing ANY Linux flavor OS
        • Start with existing CentOS installation
        • Test Appion Shared
        • Test page
        • Testing auto-installation
        • Tom Goddard visit February 2010
        • Tomo alignment appiondata
        • Troubleshooting the Web Server Shared
        • Upgrade from pre-20
        • Use Cronus3 or Fly to view your web app
        • Version200
        • Version210
        • Version220
        • Version230
        • Version300
        • Version future
        • Web Server Installation Shared
        • What does User Authentication do to myamiweb
        • Wrapper Testing
    • Leginon
        • Leginon Manual
          • An Introduction to Leginon
            • Getting Started
            • Getting Started as a Super User
            • Getting Started as a System Administrator
            • Getting Started as a basic Leginon user
            • Getting Started as a basic Leginon user in docbook version
          • 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
          • 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
        • Camera length calibration
          • Complete Installation
          • Additional Database Server Setup after Web Server Installation
          • Autoinstaller for CentOS
          • Backup Practices
          • DD Frame Alignment Server Installation
          • Database Server Installation
          • Database Server Setup to allow connection from the instruments
          • 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/Orius combo unique installation and setup
                  • Comtypes installation
                • Falcon acquire image
                  • Falcon gain correction
                  • Falcon raw frame saving configuration xml
                • Falcon raw frame saving
                • Leginon settings modification for Falcon camera
                • Using Falcon Orius combo in Leginon
                • Gatan K2 Summit Support
                • Gatan K2 Installation Notes
                  • Start DigitalMicrograph
                  • Pyscope test k2 save frames
                  • Gatan K2 installation and setup
                  • Install SerialEM DigitalMicrograph plugin
                  • Older k2 dmsem configuration
                  • Semccd installation
                • K2 Summit introduction
                • K2 calibration
                  • 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 Xmipp
            • Install supporting packages
            • 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 Redux image server
            • Install Web Server Prerequisites
            • Install phpMyAdmin
            • Install the MRC PHP Extension
              • Install the Web Interface
              • Install the Web Interface Advanced
            • Potential Problems
          • What is in this Chapter
          • Where to register and download Leginon
          • Windows Installation
          • Create and Edit Applications
          • "Calibrations" Application
          • "MSI-Edge" Application
          • "MSI-T" Application
          • "MSI-Tomography" Application
          • "MSI-raster" Application
          • "Manual" 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
          • 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
        • Database migrating exportimport scripts
          • 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
          • Upgrade processing server
          • 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
            • Check Phase Plate Patches
            • Generate Phase Plate Condition Map
            • Inspect the phase plate slot at low magnification
            • Checking Matrix and Modeled Stage Position Calibration
            • Test stage position targeting reproducibility
          • 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 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 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 MSI raster Application
          • Improving Autofocusing
          • Queuing Option - MSI-raster
          • Raster finder nodes set-up
          • Summary of this application - MSI-raster
          • 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 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
          • 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
            • MSI Operation
            • Setup Auto Square Finder using example targets
          • MSI Quick-start
          • MSI set up in more details
          • Monitor Progress of Queued Targets
          • 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 Diffraction mode TEM instrument
            • Setup df preset
            • 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
          • RCT
          • Raster Filter
          • Raster Finder
          • 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
            • Upgrade processing server
            • 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 Project Web Tool Features
            • New User Features
            • New dbemtool Web Tool Features (151)
            • 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 Developer Guide
        • Fake calibrations for Leginon simulator
        • Numextension
        • Premade Realistic-looking calibration and images for simulation
        • Setup simulator with VMware
          • Overview
          • Installation
          • Usage
          • FAQ
          • Changelog
          • Windows External Package installers
          • Windows 32 External Package Installers
          • Leginon System version beta
          • New User Features beta
          • Pyscope Changes beta
          • Leginon System version 30
          • New User Features 30
          • Pyscope Changes 30
          • Windows Camera Package Requirement
          • Protobuf installation instruction
          • SerialEM SEMCCD-GMS plugins
          • Redux
            • Using Redux to serve images on myamiweb
            • Start redux with systemd
          • Sub 3Å proteasome image shift data collection
          • Krios1-K2-NYSBC
          • Scaling Stage Position Matrix Calibration
        • Using Leginon at Scripps
        • 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)
        • Install Leginon-only Packages
        • Install SSH module for PHP webserver
        • Installation on the microscope computer 21
        • Installing comtypes
        • 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
        • Link to ubuntu
        • Linux distribution recommendation
        • Locate global config directory on Windows
        • MSI Quick-start for DD only
        • Manual Focusing Tool
        • More about Groups shared
        • Mosaic Target Maker
        • Packages installed by pysetupsh
        • PyScope Changes 22
        • Recommandation for setup at a new institute shared
        • 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 Leginon on a system where the microscope and camera are controlled by different computers
        • Using imcache to cache mrc images as jpeg images of the default size on myamiweb
        • Windows 32 External Package Installers Common
        • Windows Microscope Package Requirement
        • Windows Myami Package installers
    1. Leginon
    2. Leginon Manual
    3. An Introduction to Leginon

    An Introduction to Leginon

    1. What is the Leginon System?
    2. Terminology
    3. Graphical User Interface
    4. Supported Instrument
    5. Minimum Requirements and current NRAMM setup
    6. Getting Started

    Version Change Log >

    2025-11-18 2025-11-18
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