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An Introduction to Leginon » History » Revision 3

Revision 2 (Amber Herold, 04/14/2010 03:17 PM) → Revision 3/8 (Amber Herold, 04/14/2010 03:20 PM)

h1. An introduction to Leginon 

 # [[What is the Leginon System?]] 
 # [[Terminology]] 
 # [[Graphical User Interface]] 
 # [[Minimum Requirements and current NRAMM setup]] 
 # [[Getting Started]] 











 




 h2. What is Leginon System? 


 <abstract> 

 Leginon system include the python-side programs that are writen in python and c, the 
 MySQL database and server, and the mainly php-based image and data viewers on a web 
 server. 


 The python-side programs provide a modular framework for building applications for TEM 
 image acquisition and analysis. Nodes can be connected through abstract events in Leginon's 
 modular architecture design. This gives Leginon the flexibility of application customization 
 at multiple levels. Because nodes can be launched from different machines, Leginon's 
 applications can inherently use distributed memory systems. 


 The MySQL-side database and server keep track of all information (metadata) accompanying 
 the acquired images efficiently. 


 The php-side web server and scripts retrieve information from the database and the file 
 storage system to display both raw information and organized reports. 


 NRAMM development includes the python-side and the php-side scripts. MySQL side uses 
 directly the open-source distribution. 


 The website    "http://leginon.scripps.edu/":http://leginon.scripps.edu 
 is the central location for leginon information and links. 


 Once registed for leginon download, the users have access to the " bulletin board":http://emg.nysbc.org/bb.viewforum.php?f=2    where users and 
 developers post their questions and answers. 


 Official bug report and feature request should be entered through    "bugzilla":http://emg.nysbc.org/bugzilla/enter_bug.cgi?product=Leginon . 

 </abstract> 




 h2. Terminology 




 h2. Application 



 A Leginon application is image acquisition process that is built of several smaller 
 pieces called 'nodes'. An application defines your preferred scheme for how to acquire 
 images. An application definition includes which nodes to use, how they are connected, and 
 where they are running (possibly distributed across several machines). These three concepts 
 of applications (nodes, events, launchers) are described in more detail below. A typical 
 application involves several stages of image acquisition and image processing. Once an 
 application is designed, it can be used repeatedly for different sessions. An application 
 design can be exported for use on other Leginon installations. 





 h2. Session 



 A session is defined as an execution from start to finish of a Leginon application. All 
 data (images, results, etc.) that are created by Leginon is associated with some session. 
 The first thing a user must do when starting Leginon is create a session, or continue an 
 existing session. 





 h2. Instrument 



 An instrument is the microscope/camera system used for acquiring data during a 
 particular session. The facility at which Leginon is installed may have several different 
 microscopes, each with a unique camera setup. Each system is an instance of an 
 Instrument. 





 h2. Node 



 Nodes are the building blocks of Leginon applications. Nodes are defined for specific 
 tasks. For instance, an "Acquisition" node is designed to acquire images when it receives 
 targets from another node, which is typically some type of 'TargetFinder' node. Nodes can 
 "publish" the data they create. This means they are making their data public for other nodes 
 to use. The other nodes can "research" to find a specific item of data. Nodes may 
 communicate with each other by generating "events". 





 h2. Event 



 An event is a message sent out from a node to notify other nodes that something of 
 interest has happened. A common example is to announce that some data has been published. 
 Another example is to announce that some process has finished. The declaration of which 
 events are routed between which nodes is part of the application design process. 





 h2. Manager 



 Manager is the master of all nodes in an application. Its existence is usually 
 transparent while running a session, but it is responsible for starting up the application 
 with all its nodes and event bindings. It works behind the scenes to ensure that events are 
 properly distributed throughout the system. 





 h2. Launcher 



 A Launcher is the parent process for a set of nodes. There is typically one launcher 
 running on each machine that you intend to have nodes running on. The assignment of which 
 nodes will be started on a particular launcher is defined as part of the application. 





 h2. Preset 



 A preset is a piece of data which encapsulates the state of an instrument. At any time, 
 the current state of an instrument (magnification, image shifts, camera settings, etc) can 
 be recorded for later use. There is a particular class of Node called the PresetsManager 
 which maintains a list of presets for the current Leginon session. These presets are used by 
 other nodes to set the state of the instrument prior to acquiring an image. This allows for 
 a series of images to be acquired at a consistent state, but possibly different targets (see 
 below). This is very similar to the "Low Dose" system on many microscopes, which consists of 
 a few presets like "Search", "Focus", and "Exposure". The Leginon PresetsManager is a more 
 generalized approach which allows for and unlimited number of presets to be used (like 
 several search presets at different magnifications, or multiple exposure presets at 
 different defocus). 





 h2. Target 



 A target is a location where an image will be acquired. Targets are often selected from 
 existing images (using a TargetFinder node). Acquisition nodes are responsible for 
 interpreting Targets and then acquiring images of them. 









 h2. Graphical User Interface 




 h2. How to use this manual 



 Many places in the manual, a specific section of a window for a node on a 
 launcher/computer/instrument is mentioned. The first time they are mentioned, the full path 
 is shown as 


 computer/program window/node/subsection of the node to open the setting window/setting 
 window/section in the window> 


 It is assumed that the user knows how to follow this path to the specific section of the 
 window by reading the following graphical user interface (GUI) manual and by a little of 
 practice. A abbreviated path rather than the full path will be shown in the latter steps for 
 the same node or application. 





 h2. Leginon Window 



 The window is divided into sections. 


 * Status bar - Leginon status display such as completion of application 
 loading. 



 !http://emg.nysbc.org/software/leginon/images/images/statusbar.png! 



 * Main Menu - Submenus and options derived from Manager and Launcher 



 !http://emg.nysbc.org/software/leginon/images/images/mainmenu.png! 



 * Node Selector - Selection for the node shown in the toolbar, message log, and node 
 panel. It is also used to indicate warning by turning red for broken node. 



 !http://emg.nysbc.org/software/leginon/images/images/nodeselector.png! 



 * Error indicator !http://emg.nysbc.org/software/leginon/images/icons/error.png! - This icon will appear next to a node (in the Node Selector) that has an 
 error. 


 * Message Log Information indicator !http://emg.nysbc.org/software/leginon/images/icons/info.png! 
 - This icon will appear next to a node (in the Node Selector) that has information in 
 its message log. 


 * User Input indicator !http://emg.nysbc.org/software/leginon/images/icons/userinput.png! - This icon will appear next to a node (in the Node Selector) that 
 requires User input in order to continue processing. 


 * Processing indicator !http://emg.nysbc.org/software/leginon/images/icons/processing/green0.png! - This icon will appear next to a node (in the Node Selector) that 
 currently doing processing. 







 h2. Node Panel 





 * Node Panel - The main display/control panel for the node selected by the node 
 selector. 



 !http://emg.nysbc.org/software/leginon/images/images/nodepanel2.png! 



 * Toolbar - An area containing tools for general configuration and execution of the 
 node as well as some tools for convenience specific for individual node. 



 !http://emg.nysbc.org/software/leginon/images/images/toolbar.png! 



 * Message Log - Expandable/scrollable box showing logged information for the 
 node. 



 !http://emg.nysbc.org/software/leginon/images/images/messagelog.png! 








 h2. Parameter Entry 





 * Free entry box- For typing in either text or numbers. If in a setting window, the 
 altered entry is saved to the database when it is exited with "OK" or after 
 "Apply"/"Test". Most numerical entry accepts floating point number in any python format. 
 For example, 10.2 can also be entered as 1.02e+2. 



 !http://emg.nysbc.org/software/leginon/images/images/Entry_box.png! 



 * Restricted-entry: The user can only select a valid entry from a list. 



 !http://emg.nysbc.org/software/leginon/images/images/Entry_box_restricted.png! 



 * List box- This type of selection box select either an ordered sequence or a simple 
 unordered list. If ordered, the items in the sequence can order with "up" and "down" 
 tools. 



 !http://emg.nysbc.org/software/leginon/images/images/List_box.png! 



 * If ordered, the items in the sequence can be shifted around with "up" and "down" 
 tools. 


 * Either free or restricted entry box is used for entering a new item to the list. 
 "+" tool is used to add the entry to the list box. selecting an existing item and 
 press "-" tool removes the item from the list. 


 * Multiple items can be selected by holding down the "ctrl" or "shift" key. The 
 latter selects a range between the first and the new items. 









 h2. Image Viewing 





 * Display Panel - where the image is shown. 


 * (pixel value button) !http://emg.nysbc.org/software/leginon/images/icons/value.png! - Pixel value display tool that shows the (x,y) coordinate the intensity value at the 
 cursor. The coordinate origin is set at top-left corner. 


 * (ruler button) !http://emg.nysbc.org/software/leginon/images/icons/ruler.png! - Ruler tool that displays the distance between a reference point and the current 
 cursor position. Left click at any position inside the display panel defines the 
 reference point. 


 * (zoom button) !http://emg.nysbc.org/software/leginon/images/icons/zoom.png! 
 - Magnifying glass tool that zoom in (left click) or out (right click) at the location 
 of the cursor. 


 * (zoom selector list) !http://emg.nysbc.org/software/leginon/images/images/zoomselector.png! - Direct zoom factor selector. 


 * (cross hair button) !http://emg.nysbc.org/software/leginon/images/images/bluech.png! - Cross hair reference tool displaying a blue cross hair centered at 
 the center of the image for reference. 


 * (display range selection/input) - Contrast and brightness adjustment of the image 
 display. The default is mean +/- 5*standard deviation of image intensity. This can be 
 modified by setting the minimum (top scroll bar or entry box) and the maximaum (bottom 
 scroll bar or entry box) of the display range. 



 !http://emg.nysbc.org/software/leginon/images/images/contrbright.png! 



 * Image Stats Panel 



 !http://emg.nysbc.org/software/leginon/images/images/imstatpanel.png! 



 * Image/Target/Marker Control Panel - where the image and targets to be displayed in 
 the display panel are determined. Targets are indicated by short cross symbols or other 
 shapes of different colors. The items shown with a screen icon are of image type. Items 
 of image type can be displayed alone while markers will show only when one of the items 
 of image type is also displayed. 



 !http://emg.nysbc.org/software/leginon/images/images/imcontrolpanel.png! 



 * (status indicator) 



 <inlinegraphic 
 fileref="http://emg.nysbc.org/software/leginon/images/icons/green.png" 
 format="PNG"/> 
 <inlinegraphic 
 fileref="http://emg.nysbc.org/software/leginon/images/icons/red.png" 
 format="PNG"/> 


 - This can be either green or red. During a step-by-step testing of parameters, 
 green indicates that the step has been tested and you can proceed to the next 
 testing step. Skiping to a step below a red-indicated step will cause an 
 error. 


 * (image display tool) !http://emg.nysbc.org/software/leginon/images/icons/display.png! - Display selection. Only one of the image type can be displayed at 
 one time. 


 * (target/marker display tool) !http://emg.nysbc.org/software/leginon/images/images/target_display.png! - Display target or marker selection. Pressed down (as shown for 
 the green target) is active. More than one type of markers can be displayed on 
 layers above the image. If the markers are overlapped, the marker last to be 
 activated for display is at the top. 


 * (marker tool) !http://emg.nysbc.org/software/leginon/images/icons/arrow.png! - Marker input selection. Certain markers can be manually edited. 
 In general, these are targets for further acquisition. In such case, the marker 
 selection tool can be activated by left clicking the icon. Once activated, left 
 click in the display panel adds the marker to the image and right click removes the 
 marker pointed to. 


 * (settings) !http://emg.nysbc.org/software/leginon/images/icons/settings.png! - Settings are available for certain items in the image control 
 panel, mainly steps in automatic hole finding. Left click opens the setting window 
 and the behavior of the setting window is similar to others of the same type. 









 h2. Tool Bar 



 Tool bar of the node contains tools for setting and execution of the node functions. In 
 addition, some tools are available as pop-up for convenience. The general rule for the flow 
 of setting up and execution is to go from left to right up to the execution tool (execution 
 icon). 



 !http://emg.nysbc.org/software/leginon/images/images/toolbar.png! 






 h2. Settings Window 



 Settings windows are opened by left clicking its button !http://emg.nysbc.org/software/leginon/images/icons/settings.png! 
 in the toolbar. Note that only one setting swindow can be opened at a time and that all 
 functions in the main leginon window is inactivated when a settings window is open even if 
 the leginon window is the focus. The content of the settings window depends on the purpose 
 of the settings. The general controls are described here: 


 * Test: found in settings of image processing steps. When clicked, the current setting 
 in the window is saved to database and applied to the current input and the results 
 saved as its output. If the item output is displayed in the node display panel, the 
 content will be changed accordingly. 



 !http://emg.nysbc.org/software/leginon/images/images/test.png! 



 * Apply: save the modified setting to database for future execution but not the 
 current test input. It is activated only if the modification of the input is completed, 
 normally by pressing the Enter key on the keyboard. Since current GUI does not allow 
 changes to the main window to be made while setting window is on, Using button is not 
 necessary since "OK" button will save the settings anyway. 



 !http://emg.nysbc.org/software/leginon/images/images/apply.png! 



 * Cancel: close the setting window and revert the setting to the last saved values. 
 This means you can not cancel setting modification if you have "test"ed or "apply"ed the 
 settings. 



 !http://emg.nysbc.org/software/leginon/images/images/cancel.png! 



 * OK or Done: close the setting window and save all modified settings to the 
 database. 



 !http://emg.nysbc.org/software/leginon/images/images/ok.png! 








 h2. Execution tools 



 Found in the node toolbar. They may take on different meanings for different node 
 classes. The general ones are described here: 


 * (Execute/Submit button) !http://emg.nysbc.org/software/leginon/images/icons/play.png! 
 : Perform one of the four possible functions if available and active for a node: 


 * When the application is in standby, it executes, sometimes with setting up the 
 main function of the node. 


 * When the application is running automatically, it indicates that the node is in 
 use. 


 * When the application is paused for user input, it submit the user approved 
 inputs and continue on the flow. 


 * When the application is paused by the "pause" tool in the same node, it removes 
 the pause flag and continue on the application flow. 




 * (Pause button) !http://emg.nysbc.org/software/leginon/images/icons/pause.png! : Pause data processing flow when the current input in a queue list is done. 


 * (Abort button) !http://emg.nysbc.org/software/leginon/images/icons/stop.png! 
 : Abort all data processing of the whole list in the queue. 









 h2. Minimum Requirement and current NRAMM setup 



 *Recommendation is based on the current NRAMM setup 



 h2. Electron Microscope with its Controling Computer 



 FEI Tecnai 12 with Scripting SW, network connected, and the ability to install software 
 on it 





 h2. CCD 



 Gatan, or Tietz-minimal 1kx1k; NRAMM 4kx4k 





 h2. A Second Computer 




 h2. CPU 



 Minimal 1 GHz; NRAMM AMD Athlon 64 FX-60 Dual Core 2.6 GHz 





 h2. RAM 



 Minimal 1 GB physical memory and 1GB swap; NRAMM 4GB physical memory and 2GB 
 swap 





 h2. Hard drive 



 10 GB for the softwares and maybe a few hours worth of data collection. Much larger 
 for routine use. NRAMM 15Tb and growing 





 h2. Network connection 



 100 Mbps; NRAMM 1 Gbps 







 h2. Leginon system components developed at Leginon home 



 Leginon Home:    "http://www.leginon.org/":http://www.leginon.org/ 





 h2. Supporting packages and programs available through internet or you Linux 
 distribution 



 There are minimum of ten packages or single programs, some of them are included in your 
 Linux distribution. 







 h2. Leginon supporting programs available upon request 



 adaexp.exe that is required if film exposure is to be made through Leginon on FEI Tecnai 
 machines is available by request. Please contact Max Otten: <email>mto@nl.feico.com</email> 
 and let him know what version of the Tecnai user interface you are using. 









 h2. Getting Started 




 h2. Full (Super User) Manual - Getting Started 



 These steps are a general overview of walking through the entire procedure involving 
 installation, microscope alignment, calibrations, and using Leginon applications (e.g. 
 Manual, Calibrations, MSI). 



 h2. Download Leginon System 


 "http://www.leginon.org/":http://www.leginon.org/ 





 h2. Install Leginon System 



 Refer to the <link linkend="completeinstall">Complete Installation</link> 





 h2. Add Users, Groups, Instruments, Calibrations, and Applications 



 Refer to <link linkend="addusers">Administration</link> 


 For advanced Leginon users who would like to create an application, see the <link 
 linkend="createapp">application creation chapter</link>. 





 h2. Test run 



 Refer to <link linkend="runleg_chapter">Start Leginon</link> chapter for test run on 
 the microscope and on a remote computer. 





 h2. Align the microscope 



 Refer to <link linkend="microscope_setup">Microscope Set-up</link> 





 h2. Calibrate Leginon for the microscope 



 Refer to the <link linkend="calapp_chapter">Calibrations chapter</link> 





 h2. Set-up and Run MSI 



 Refer to <link linkend="MISQuickStart">MSI quick set-up checklist</link> 


 AND 


 Refer to <link linkend="leg1operation">MSI Operation</link> 





 h2. Help yourself and others 



 Refer to <link linkend="Inst_troubleshooting">Installation Trouble Shooting</link>, 
 <link linkend="MSI_troubleshooting">User Trouble Shooting</link> and Leginon    "Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=2 . 







 h2. Know the details 



 For advanced Leginon users who would like to create an application, see the <link 
 linkend="createapp">application creation chapter</link>. 


 Refer to <link linkend="Nodes">Node Description</link> 







 h2. Installation (System Administrator) - Getting Started 



 These steps are geared soley towards the system administator(s) that will installing 
 Leginon and setting it up initially for the rest of the Leginon users that need not be 
 concerned with these details. 


 Refer to <link linkend="Inst_troubleshooting">Installation Trouble Shooting</link>, and 
 Leginon    "Bulletin 
 Board":http://emg.nysbc.org/bb/viewforum.php?f=2 . 



 h2. Download Leginon System 



 Leginon Home:    "http://www.leginon.org/":http://www.leginon.org/ 


 Direct links to downloads: 


 *    "http://emg.nysbc.org/software/leginon/":http://emg.nysbc.org/software/leginon/ 


 *    "http://emg.nysbc.org/software/dbemtools/":http://emg.nysbc.org/software/dbemtools/ 


 *    "http://emg.nysbc.org/software/mrctools":http://emg.nysbc.org/software/mrctools . 







 h2. Install Leginon System 



 Refer to the <link linkend="completeinstall">Complete Installation</link> 





 h2. Add Users, Groups, Instruments, Calibrations, and Applications 



 Refer to <link linkend="addusers">Administration</link> 





 h2. Test run 



 Refer to <link linkend="runleg_chapter">Start Leginon</link> chapter for test run on 
 the microscope and on a remote computer. 







 h2. Short Manual (Basic Leginon User) - Getting Started 



 These steps are intended to help the basic Leginon user who will operate Leginon (and 
 not care about installation or the first-time calibrations). 



 h2. Align the microscope 



 Refer to <link linkend="microscope_setup">Microscope Set-up</link> 





 h2. Recording images with Low Dose Kit on the microscope 



 Refer to using the <link linkend="manual_app">Manual</link> application 





 h2. Set-up and run MSI 



 Refer to <link linkend="MISQuickStart">MSI quick set-up checklist</link> 


 AND 


 Refer to <link linkend="leg1operation">MSI Operation</link> 





 h2. Help yourself and others 



 Refer to <link linkend="MSI_troubleshooting">User Trouble Shooting</link>