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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
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
Leginon Developer Guide
Fake calibrations for Leginon simulator
Numextension
Premade Realistic-looking calibration and images for simulation
Setup simulator with VMware
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
Leginon
Miscellaneous
Leginon System version beta
New User Features beta
None.
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