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Myami Documentation
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    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. Installation Troubleshooting

    Troubles with Imaging

    • Reference image from other users not readable( See Operation Trouble Shooting)

    • Navigator does not move the stage after a pyScope update on the computer controlling the microscope

    < Network problems | Troubles with Calibrations >

    2025-11-18 2025-11-18
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