Leginon

h1. The EM node

The EM node or tab is the node that is running on the microscope computer. This node is

responsible for communicating to the microscope, CCD, and Leginon. Without the EM node,

Leginon cannot control the microscope.

Required bindings: None

h2. Microscope paramters

Select TEM to view and sometimes change microscope parameters

*  Leginon/EM> Do Pauses

enabled = pause for example 2s before acquiring an image (pauses set in acquisition

nodes)

*  Leginon/EM> High Tension

*  Leginon/EM> Magnification

*  Leginon/EM> Intensity

*  Leginon/EM> Spot size

*  Leginon/EM> Lenses: Objective excitation

*  Leginon/EM> image shift (x, y)

*  Leginon/EM> image shift raw (x, y)

*  Leginon/EM> beam shift (x, y)

*  Leginon/EM> beam tilt (x, y)

*  Leginon/EM> objective stigmator (x, y)

*  Leginon/EM> diffraction stigmator (x, y)

*  Leginon/EM> condensor stigmator (x, y)

*  Leginon/EM> focus (absolute focus value)

*  Leginon/EM> defocus (relative focus value)

*  Leginon/EM> reset defocus (enabling resets the defocus)

*  Leginon/EM> Vacuum Status

*  Leginon/EM> Column pressure (in Pa)

*  Leginon/EM> Column valves ("open" or "closed")

*  Leginon/EM> Turbo pump ("on" or "off")

* Leginon/EM> Stage Status ("busy, ready, or unknown", cannot manually

adjust)

*  Leginon/EM> Correct stage movement (enabled)

*  Leginon/EM> Stage Position x/y/z

*  Leginon/EM> Angle a/b

*  Leginon/EM> Film Stock

*  Leginon/EM> Film Exposure number (of the next exposure)

*  Leginon/EM> Film Exposure type ("manual")

*  Leginon/EM> Automatic exposure time (s, based on intensity)

*  Leginon/EM> Manual exposure time

*  Leginon/EM> User code (that will appear on the next film exposure)

*  Leginon/EM> Date Type (YY.MM.DD)

*  Leginon/EM> Text (additional text to apply to the next film exposure)

*  Leginon/EM> Shutter (pre-specimen, "open" or "closed")

*  Leginon/EM> External shutter (post specimen shutter connection, "connected" or

"disconnected")

*  Leginon/EM> Screen Current (mA)

*  Leginon/EM> Screen Position (Main and Small) ("up" or "down")

*  Leginon/EM> Holder Status ("inserted" or "not inserted")

*  Leginon/EM> Holder Type (options "single tilt, no holder, cryo, unknown

holder")

*  Leginon/EM> Lose Dose Status ("on" or "off", default is "off"*)

*  Leginon/EM> Low Dose Mode ("exposure*, focus, or search")

*  Leginon/EM> film stock

h2. Camera parameters

The current camera parameters are displayed in Leginon/EM>

Information:

*  Leginon/EM> binning (x, y)

*  Leginon/EM> Size (x,y)

*  Leginon/EM> Pixel size (x,y)

*  Leginon/EM> Name

*  Leginon/EM> Chip

*  Leginon/EM> Serial number

*  Leginon/EM> Maximum value

*  Leginon/EM> Live mode

*  Leginon/EM> Simulation image path

*  Leginon/EM> Temperature

*  Leginon/EM> Harware gain index

*  Leginon/EM> Hardware speed index

*  Leginon/EM> Retractable

*  Leginon/EM> Axis

Settings:

*  Leginon/EM> Dimension (x, y)

*  Leginon/EM> Offset (x,y) (from the top left corner of the CCD)

*  Leginon/EM> Binning (x,y)

*  Leginon/EM> Pre-configured camera settings

*  Leginon/EM> Custom configuration

*  Leginon/EM> Exposure time (ms)

*  Leginon/EM> Exposure type ("normal" or "dark")

*  Leginon/EM> Gain index

*  Leginon/EM> Speed index (the read-out speed of the CCD)

*  Leginon/EM> Mirror

*  Leginon/EM> Rotate

*  Leginon/EM> Shutter open delay

*  Leginon/EM> Shutter close delay

*  Leginon/EM> Preamp delay

*  Leginon/EM> Parallel mode