Leginon

h1. Terminology

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.