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Appion
Leginon

Myami Documentation

leginon-org/leginon

Appion
Appion
- Appion Manual
  Appion Manual
  - Appion Manual
  - An Introduction to Appion
    An Introduction to Appion
    
    An Introduction to Appion
    
    Authors
    
    What is Appion
  - Appion User Guide
    Appion User Guide
    
    Appion User Guide
    
    Administration Tools Guide
    
    Appion Processing
    Appion Processing
    
    Appion Processing
    
    Ab Initio Reconstruction
    Ab Initio Reconstruction
    
    Ab Initio Reconstruction
    
    EMAN Common Lines
    
    IMAGIC Angular Reconstitution
    
    OTR Volume
    
    RCT Volume
    
    CTF Estimation
    CTF Estimation
    
    CTF Estimation
    
    Ace 2 Estimation
    
    Ace Estimation
    Ace Estimation
    
    Ace Estimation
    
    Ace script
    
    Aceman
    
    CtfFind Estimation
    
    Phase plate CTF Estimation
    
    Common Workflow
    Common Workflow
    
    Common Workflow
    
    Quality Assessment
    
    Random-Conical Tilt (RCT) Reconstruction workflow
    
    Step by Step Guide
    
    Trimer processing workflow
    
    CryoSPARC
    
    Direct Detector Frame Processing
    Direct Detector Frame Processing
    
    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
    Image Assessment
    
    Image Assessment
    
    Multi Img Assessment
    
    Run Image Rejector
    
    Web Img Assessment
    
    Import Tools
    Import Tools
    
    Import Tools
    
    EMDB to Model
    
    PDB to Model
    
    PDB tp Model
    
    Upload Model
    
    Upload More Images
    Upload More Images
    
    Upload More Images
    
    Upload image grouping
    
    Upload Particles
    
    Upload Stack
    
    Upload Template
    
    Particle Alignment
    Particle Alignment
    
    Particle Alignment
    
    Run Alignment
    Run 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
    Run Feature Analysis
    
    Run Feature Analysis
    
    Spider Coran Classification
    
    Xmipp Kerden Self-Organizing Map
    
    Xmipp Rotational Kerden Self-Organizing Map
    
    Run Particle Clustering
    Run Particle Clustering
    
    Run Particle Clustering
    
    Hierarchical or K-means Clustering
    
    Particle Selection
    Particle Selection
    
    Particle Selection
    
    Dog Picking
    
    Manual Picking
    
    Random Conical Tilt Picking
    Random Conical Tilt Picking
    
    Random Conical Tilt Picking
    
    Align and Edit Tilt Pairs
    
    Auto Align Tilt Pairs
    
    Template Picking
    
    Processing Cluster Login
    
    Refine Reconstruction
    Refine Reconstruction
    
    Refine Reconstruction
    
    EMAN Refinement
    
    Frealign Refinement
    
    IMAGIC Refinement
    
    Refinement Post-processing Procedures
    
    SPIDER Refinement
    
    Region Mask Creation
    Region Mask Creation
    
    Region Mask Creation
    
    Crud Finding Crud Finding
    Table of contents
    
    General Workflow:
    
    Notes, Comments, and Suggestions:
    
    Manual Masking
    
    Maskiton
    
    Repeat from other session
    
    Stacks
    Stacks
    
    Stacks
    
    More Stack Tools
    More Stack Tools
    
    More Stack Tools
    
    Combine Stacks
    
    Convert Stack into Particle Picks
    
    Jumpers SubStack
    
    View Stacks
    View Stacks
    
    View Stacks
    
    Center Particles
    
    Create Substack
    
    Filter by MeanStdev
    
    Sort Junk
    
    Stack Creation
    
    Synthetic Data
    Synthetic Data
    
    Synthetic Data
    
    Synthetic Dataset Creation
    
    Terminology
    
    Tomography
    Tomography
    
    Tomography
    
    Align Tilt-Series
    
    Align tilt series
    
    Create full tomogram
    
    Create tomogram subvolume
    Create tomogram subvolume
    
    Create tomogram subvolume
    
    Average tomogram subvolumes
    
    Upload full tomogram
    
    Upload Refinement
    
    Xmipp 3 Clustering 2D Alignment
    
    Appion and Leginon Database Tools
    Appion and Leginon Database Tools
    
    Appion and Leginon Database Tools
    
    Administration
    Administration
    
    Administration
    
    Applications
    
    Goniometer
    
    Groups
    
    Instruments
    
    Revert Settings
    
    Users
    
    Hole Template Viewer
    
    Image Viewers
    Image Viewers
    
    Image Viewers
    
    2 Way Viewer
    
    3 Way Viewer
    
    Common Features
    
    Dual Viewer
    
    Image Viewer
    
    RCT viewer
    
    LOI - Leginon Observer Interface
    
    Project DB
    Project DB
    
    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
    Upload Images to a new Project Session
    
    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
    User Management
    
    User Management
    
    Enable User Authentication
    
    Logout
    
    Modify Your Profile
    
    New User Registration
    
    Retrieve Forgotten Password
    
    Appion output
  - Complete Installation
    Complete Installation
    
    Complete Installation
    
    Additional Database Server Setup after Web Server Installation
    
    Changes to auto-installed appion for production usage
    
    Create a Test Project
    Create a Test Project
    
    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
    Processing Server Installation
    
    Processing Server Installation
    
    Compile FindEM
    Compile FindEM
    
    Compile FindEM
    
    Install FindEM from source
    
    Compile Radermacher
    
    Configure appioncfg
    
    Configure leginoncfg
    
    Configure sinedoncfg
    
    Download Appion Files
    
    Explanation of Sample Names
    
    Install Ace2
    Install Ace2
    
    Install Ace2
    
    Compile Ace2 from source
    
    Install Appion Packages
    
    Install EMAN
    
    Install EM Hole Finder
    
    Install External Packages
    Install External Packages
    
    Install External Packages
    
    Install MotionCor2
    
    Install Imod
    
    Install Protomo
    
    Install Protomo2
    
    Install SIMPLE
    
    Install SPIDER
    
    Install UCSF Chimera
    
    Install Xmipp
    
    Install dosefgpu driftcorr
    Install dosefgpu driftcorr
    
    Install dosefgpu driftcorr
    
    Install motioncor2 shared
    
    Install supporting packages
    
    Perform system check
    
    Test Appion
    
    Security Considerations
    
    Select Linux distribution to use
    
    Setup Remote Processing
    Setup Remote Processing
    
    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
    Web Server Installation
    
    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
    Install the MRC PHP Extension
    
    Install the MRC PHP Extension
    
    Troubleshooting Notes
    
    Install the Web Interface
    Install the Web Interface
    
    Install the Web Interface
    
    Install the Web Interface Advanced
    
    Potential Problems
    
    Start NFS
  - Upgrade Instructions
    Upgrade Instructions
    
    Upgrade Instructions
    
    Minor release update
    
    Upgrade From 20x
    
    Upgrade From 21x
    
    Upgrade From 22-redux
    
    Upgrade From 22x
    
    Upgrade From 30 or above
    Upgrade From 30 or above
    
    Upgrade From 30 or above
    
    New support package requirement for 33
  - Version Change Log
    Version Change Log
    
    Version Change Log
    
    Version 32 Change Log
- Developers guide
  Developers guide
  - Developers guide
  - AMI Eclipse Quick Start Guide
    AMI Eclipse Quick Start 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
    Coding Best Practices
    
    Coding Best Practices
    
    Code Review Guide
    Code Review Guide
    
    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 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
- Miscellaneous
  Miscellaneous
  - EMG Redmine Quick Start Guide
    EMG Redmine Quick Start Guide
    
    EMG Redmine Quick Start Guide
    
    Issue Workflow Tutorial
    
    Wiki Tips
  - Install Appion and Leginon using the auto-installation tool share
    Install Appion and Leginon using the auto-installation tool share
    
    Install Appion and Leginon using the auto installation tool share
    
    Reconfigure the database
    
    Regkey request
  - Processing Server External Packages Installation
    Processing Server External Packages Installation
    
    Processing Server External Packages Installation
    
    External Package requirement of Appion scripts
    
    Package executable alias name in Appion
    Package executable alias name in Appion
    
    Package executable alias name in Appion
    
    Package alias table
  - CentOS6 installation
    CentOS6 installation
    
    CentOS6 installation
    
    Install Free-Hand Test
    Install Free-Hand Test
    
    Install Free Hand Test
    
    FreeHand compile
  - Download Appion Files Shared
    Download Appion Files Shared
    
    Download Appion Files Shared
    
    Currrent myami release
  - Install supporting packages Shared
    Install supporting packages Shared
    
    Install supporting packages Shared
    
    Extra supporting package table
  - Linux distribution recommendation
    Linux distribution recommendation
    
    Linux distribution recommendation
    
    Link to ubuntu
  - Web Server Installation on CentOS 6
    Web Server Installation on CentOS 6
    
    Web Server Installation on CentOS 6
    
    Current myami release checkout
  - 2010 Appion Developer Workshop
    2010 Appion Developer Workshop
    
    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
- Leginon Manual
  Leginon Manual
  - Leginon Manual
  - An Introduction to Leginon
    An Introduction to Leginon
    
    An Introduction to Leginon
    
    Getting Started
    Getting Started
    
    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
    Minimum Requirements and current NRAMM setup
    
    Minimum Requirements and current NRAMM setup
    
    Buffer(Ingestion) Server setup
    
    Compatible Instrument
    
    Current NRAMM setup
    Current NRAMM setup
    
    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
    Supported Instrument
    
    Supported Instrument
    
    JEOL 1230 installation specifics
    
    Terminology
    
    What is the Leginon System
  - Administration Tools
    Administration Tools
    
    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
    Complete Installation
    
    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 instrument computers
    
    Installation on the instrument computers
    
    Installation on the camera computer
    Installation on the camera computer
    
    Installation on the camera computer
    
    Ceta camera support
    
    Direct Electron DE-12 direct detection device support
    Direct Electron DE-12 direct detection device 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 camera support
    
    Falcon camera support
    
    Falcon Orius combo installation and setup
    Falcon Orius combo installation and setup
    
    Falcon/Orius combo unique installation and setup
    
    Comtypes installation
    
    Falcon acquire image
    
    Falcon gain correction
    Falcon gain correction
    
    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 Summit Support
    
    Gatan K2 Summit Support
    
    Gatan K2 Installation Notes
    
    Gatan K2 Installation Pyscope Test
    Gatan K2 Installation Pyscope Test
    
    Start DigitalMicrograph
    
    Pyscope test k2 save frames
    
    Gatan K2 installation and setup
    Gatan K2 installation and setup
    
    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 DDD movie stack
    
    Make DDD movie stack
    
    Make movie stack with darkbrightnormgain references yourself without LeginonAppion libraries
    
    Using Gatan K2 Summit in Leginon
    Using Gatan K2 Summit in Leginon
    
    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 and setup
    
    Gatan K3 installation and setup
    
    Gatan K3 Installation Pyscope Test
    
    Gatan K3 Instrumentscfg
    
    Gatan on Windows-32
    Gatan on Windows-32
    
    Gatan on Windows 32
    
    Gatan on Windows-32 with TecnaiCCDdll
    
    Gatan on Windows with semccddll
    Gatan on Windows with semccddll
    
    Gatan on Windows with semccddll
    
    Dm camera configuration
    
    Gatan UltraScan dmsem Installation Pyscope Test
    Gatan UltraScan dmsem Installation Pyscope Test
    
    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
    Installation on the microscope computer 30
    
    Installation on the microscope computer 30
    
    FEI Talos installation specifics
    
    FEI TecnaiTitan installation specifics
    FEI TecnaiTitan installation specifics
    
    FEI TecnaiTitan installation specifics
    
    Setup feicfg
    
    Unable to initializ Tecnai interface error
    Unable to initializ Tecnai interface error
    
    Unable to initializ Tecnai interface error
    
    Find and register a dll file as command components in Windows
    
    JEOLCOM installation specifics
    JEOLCOM installation specifics
    
    JEOLCOM installation specifics
    
    JEOL External3 setup
    
    Leginon Operation for JEM scopes
    
    Setup and Calibration for jeolcfg
    Setup and Calibration for jeolcfg
    
    Setup and Calibration for jeolcfg
    
    J2100f k2 preset design
    
    J3200 de20 preset design
    
    Trouble shooting with Python IDLE
    
    Windows General Package Requirement
    Windows General Package Requirement
    
    Windows General Package Requirement
    
    Git for windows cloning
    
    Git for windows installation
    
    Windows myami svn checkout
    
    Windows Installation All
    Windows Installation All
    
    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
    Installation on the microscope computer
    
    Installation on the microscope computer
    
    Auoit program script compilation
    
    Network Configuration
    Network Configuration
    
    Network Configuration
    
    An example of working port-forwarding configuration
    
    Ports used by Leginon
    
    Next Steps
    
    Possible Computer Set-up Configurations
    
    Processing Server Installation
    Processing Server Installation
    
    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
    Select Linux distribution to use
    
    Select Linux distribution to use
    
    Instructions for installing CentOS on your computer
    
    Web Server Installation
    Web Server Installation
    
    Web Server Installation
    
    Check php information
    Check php information
    
    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
    
    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
    Create and Edit Applications
    
    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
    Data Collection Setup Examples
    
    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
    Sub-3Å proteasome stage-shift data collection
    
    Sub 3Å proteasome stage shift data collection
    
    Krios-K2-TSRI Presets
  - Database migrating exportimport scripts
  - Frequent Asked Questions
    Frequent Asked Questions
    
    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)
    How to Update from v32 (Instrument Windows Computer)
    
    How to Update from v32 Instrument Windows Computer
    
    Tecnai to fei Instrumentscfg change
  - How to Update from v34 (Linux)
    How to Update from v34 (Linux)
    
    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
    Installation Troubleshooting
    
    Installation Troubleshooting
    
    Administration Tool problems
    
    Getting Help
    
    InstallationUpdate problems
    
    Network problems
    
    Test run operation problems
    
    Troubles with Calibrations
    
    Troubles with Imaging
  - Instrument Set-up
    Instrument Set-up
    
    Instrument Set up
    
    Calibrations required on FEI microscopes
    Calibrations required on FEI microscopes
    
    Calibrations required on FEI microscopes
    
    HM Beam Shift Image Shift Calibration
    
    TEM Scripting Beam Tilt Calibration
    TEM Scripting Beam Tilt Calibration
    
    TEM Scripting Beam Tilt Calibration
    
    Running get beamtiltscalepy
    
    Calibrations required on the microscope alone before starting Leginon
    Calibrations required on the microscope alone before starting Leginon
    
    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 Usage Specifics
    
    Instrument Usage Specifics
    
    Instrument Selection
    Instrument Selection
    
    Instrument Selection
    
    Camera Configuration
    Camera Configuration
    
    Camera Configuration
    
    Saving frames from direct detectors
  - Lacey Carbon Application
    Lacey Carbon Application
    
    Lacey Carbon Application
    
    RasterFC Finder node set-up
    
    RasterFC Lacey carbon rastering
    RasterFC Lacey carbon rastering
    
    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
    Leginon "Calibrations" Application
    
    Leginon Calibrations Application
    
    Apply Extra rotation
    
    Autofocus Calibration with Beam Tilt Node
    
    Beam Shift matrix calibration
    
    Beam Size Calibration
    
    Bright and Dark reference images
    Bright and Dark reference images
    
    Bright and Dark reference images
    
    Using image shift matrix calibration to refine image shift scale in jeolcfg
    
    Calibration without presets
    
    Check Phase Plate Patches
    Check Phase Plate Patches
    
    Check Phase Plate Patches
    
    Generate Phase Plate Condition Map
    
    Inspect the phase plate slot at low magnification
    
    Checking Matrix and Modeled Stage Position Calibration
    Checking Matrix and Modeled Stage Position Calibration
    
    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
    Image Shift matrix calibration
    
    Image Shift matrix calibration
    
    Refine IMAGE SHIFT SCALE in jeolcfg
    
    Importance of making calibrations
    
    Lens Aberration Correction Calibration for Beam-Image Shift Targeting
    Lens Aberration Correction Calibration for Beam-Image Shift Targeting
    
    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
    Stage Position matrix calibration
    
    Stage Position matrix calibration
    
    Scaling Stage Position Matrix
    
    Startup Calibrations
  - Leginon "MSI-Edge" Application
    Leginon "MSI-Edge" Application
    
    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
    Leginon "MSI-RCT" and MSI-RCT raster" Applications
    
    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
    Summary of this application - MSI-RCT
    
    Summary of this application MSI RCT
    
    Good negative stained images for RCT
  - Leginon "MSI-T" Application
    Leginon "MSI-T" Application
    
    Leginon MSI T Application
    
    Creating Hole Template
    
    Exposure Targeting Set-up for MSI-T
    
    Exposure Targeting Set-up for MSI-T for Four holes
    Exposure Targeting Set-up for MSI-T for Four holes
    
    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
    Leginon "MSI-T-Tilt" Application
    
    Leginon MSI T Tilt Application
    
    MSI-T-Tilt Installation
    
    MSI-T-Tilt Operation
    
    Summary of this application - MSI-T-Tilt
  - Leginon "MSI-Tomography" Application
    Leginon "MSI-Tomography" Application
    
    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
    Leginon "MSI-raster" Application
    
    Leginon MSI raster Application
    
    Improving Autofocusing
    
    Queuing Option - MSI-raster
    
    Raster finder nodes set-up
    
    Summary of this application - MSI-raster
  - Leginon "Manual Application"
    Leginon "Manual Application"
    
    Leginon Manual Application
    
    Advanced Features
    
    Running "Manual" Application
    
    Startup
    
    The Application
    
    Using the Web viewer
    Using the Web viewer
    
    Using the Web viewer
    
    2 Way Viewer
    
    3 Way Viewer
    
    Common Features
    
    Dual Viewer
    
    Image Tools
    
    Image Viewer
  - Leginon "Robot-MSI-Screen" Applications
    Leginon "Robot-MSI-Screen" Applications
    
    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
    Leginon "RobotMSI-Section" Application
    
    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
    Leginon System version 31
    
    Leginon System version 31
    
    New User Features 31
    New User Features 31
    
    New User Features 31
    
    Child Imaging Area and Beam Diameter Display in TargetFinder Nodes
    
    Pyscope Changes 31
  - Leginon System version 32
    Leginon System version 32
    
    Leginon System version 32
    
    New User Features 32
    
    Pyscope Changes 32
    Pyscope Changes 32
    
    Pyscope Changes 32
    
    JEOL scope support
  - Leginon System version 33
    Leginon System version 33
    
    Leginon System version 33
    
    New User Features 33
    New User Features 33
    
    New User Features 33
    
    How often should the phase plate moved to the next patch
    
    Ice Thickness Measurement using Energy Filter
    Ice Thickness Measurement using Energy Filter
    
    Ice Thickness Measurement using Energy Filter
    
    Introduction and description of method
    
    Notes on Use
    
    Parameters needed
    
    MSI-PP Appplication
    
    Slack notification for Leginon errors
    Slack notification for Leginon errors
    
    Slack notification for Leginon errors
    
    Activate Slack notifications in Leginon
    
    Special Beam Tilt Calibration for Phase Plate
    
    Volta Phase Plate Usage
    Volta Phase Plate Usage
    
    Volta Phase Plate Usage
    
    Phase Plate Aligner Node Class
    Phase Plate Aligner Node Class
    
    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
    Leginon System version 36
    
    Leginon System version 36
    
    Pyscope Changes 36
    
    Sinedon Changes 36
  - Leginon System version 37
    Leginon System version 37
    
    Leginon System version 37
    
    New User Features
  - Leginon System version pymysql
    Leginon System version pymysql
    
    Leginon System version pymysql
    
    Install pymysql on Windows PC
  - Multi-Scale Imaging Applications in General
    Multi-Scale Imaging Applications in General
    
    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
    Iterative Stage Movement
    
    Iterative Stage Movement
    
    Determine Target Tolerance and Acceptable Tolerance
    
    MSI Operation
    MSI Operation
    
    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
    Pre-MSI Set-up
    
    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
    Ways of Moving to Targets in Nodes that acquire images inside MSI
    
    Ways of Moving to Targets in Nodes that acquire images inside MSI
    
    Image Beam Shift matrix calibration
  - New User Features 34
    New User Features 34
    
    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
    New User Features 35
    
    New User Features 35
    
    Aperture selection through tem controller
    
    Continuous tilt electron diffraction recording
    Continuous tilt electron diffraction recording
    
    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
    Tivips f416 electron diffraction recording
    
    Tivips f416 electron diffraction recording
    
    Create Leginon view port
  - New User Features 36
    New User Features 36
    
    New User Features 36
    
    Appion autoRelauncher
    
    Falcon 4 EER integration
    Falcon 4 EER integration
    
    Falcon 4 EER integration
    
    Import falcon4 gain reference from TFS program
    
    Setup falcon4 eer
    
    Multi-grid autoscreening
    Multi-grid autoscreening
    
    Multi grid autoscreening
    
    Check list for each autoscreening run
    
    First-time autoscreening setup
    First-time autoscreening setup
    
    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
    Node Descriptions
    
    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
    Preferences Setup
    
    Preferences Setup
    
    Initial MSI application preference setup
    
    Krios Leginon Preferences
    
    MSI-Tomography Preferences
    MSI-Tomography Preferences
    
    MSI Tomography Preferences
    
    Set up dose parameters in Tomography
    
    Robot MSI-Section preference set-up
  - PyScope Changes 34
  - PyScope Changes 35
    PyScope Changes 35
    
    PyScope Changes 35
    
    Direct assignment of frame fliprotation in dmsemcfg for Gatan K2 and K3 cameras
    
    Falcon 4 support
    
    Hitachi 7800 support
    Hitachi 7800 support
    
    Hitachi 7800 support
    
    Hitachi install
    Hitachi install
    
    Hitachi install
    
    Setup and Calibration for hhtcfg and focus offset
    
    Hitachi setup
    
    Leginon Operation for HT7800
  - Start Leginon
    Start Leginon
    
    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
    Test Network Connection Between Remote and Instrument Computers
    
    Test Network Connection Between Remote and Instrument Computers
    
    Configure pyamicfg for host-ip pairings
    
    Reorder the network connections
  - Trouble shooting
    Trouble shooting
    
    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
    Upgrade Instructions
    
    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
    Upgrade to Leginon System version 16
    
    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
    Upgrade to Leginon System version 21 from version 20
    
    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
    Upgrade to Leginon System version 22 from version 21
    
    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
    Upgrade to Leginon System version 2x from version 16
    
    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
    Upgrade to Leginon System version 30 from version 22
    
    Upgrade to Leginon System version 30 from version 22
    
    How to Update from v22 (Linux)
  - Upgrade to Leginon System version 31 from version 30
    Upgrade to Leginon System version 31 from version 30
    
    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 to Leginon System version 32 from version 31
    
    Upgrade to Leginon System version 32 from version 31
    
    How to Update from v31 (Linux)
    How to Update from v31 (Linux)
    
    Upgrade processing server
    
    How to Update from v31 (Instrument Windows Computer)
  - Upgrade to Leginon System version 33 from version 32
    Upgrade to Leginon System version 33 from version 32
    
    Upgrade to Leginon System version 33 from version 32
    
    How to Update from v32 (Linux)
  - Upgrade to Leginon System version 34 from version 33
    Upgrade to Leginon System version 34 from version 33
    
    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
    Using FEI Titan Krios in Leginon
    
    Using FEI Titan Krios in Leginon
    
    Auto Nitrogen Filler Triggering
  - Using Project Management Tools
    Using Project Management Tools
    
    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
    Version Change Log
    
    Version Change Log
    
    Leginon System version 1 6
    Leginon System version 1 6
    
    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
    Leginon System version 20
    
    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
    Leginon System version 21
    
    Leginon System version 21
    
    Known Bugs 21
    
    New User Features 21
    
    New Web Tool Features 21
    
    Leginon System version 22
    Leginon System version 22
    
    Leginon System version 22
    
    New User Features 22
- Leginon Developer Guide
  Leginon Developer Guide
- Miscellaneous
  Miscellaneous
  - TiltPicker
    TiltPicker
    
    Overview
    
    Installation
    
    Usage
    
    FAQ
    
    Changelog
  - Windows External Package installers
    Windows External Package installers
    
    Windows External Package installers
    
    Windows 32 External Package Installers
  - Leginon System version beta
    Leginon System version beta
    
    Leginon System version beta
    
    New User Features beta
    
    Pyscope Changes beta
  - Leginon System version 30
    Leginon System version 30
    
    Leginon System version 30
    
    New User Features 30
    
    Pyscope Changes 30
  - Windows Camera Package Requirement
    Windows Camera Package Requirement
    
    Windows Camera Package Requirement
    
    Protobuf installation instruction
    
    SerialEM SEMCCD-GMS plugins
  - Redux
    Redux
    
    Redux
    
    Using Redux to serve images on myamiweb
    Using Redux to serve images on myamiweb
    
    Using Redux to serve images on myamiweb
    
    Start redux with systemd
  - Sub-3Å proteasome image-shift data collection
    Sub-3Å proteasome image-shift data collection
    
    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

Table of contents

General Workflow:
Notes, Comments, and Suggestions:

Appion
Appion Manual
Appion User Guide
Appion Processing
Region Mask Creation

Crud Finding

General Workflow:

Notes, Comments, and Suggestions:

< Region Mask Creation | Manual Masking >

2025-12-10 2025-12-10

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