Property File Entries

Many parameters can be set in SerialEM through the properties file. They all have default values in the program, and in most cases the values in the properties file are the defaults. A property is entered by having a line with a keyword followed by one or more values. As of SerialEM 2.6.0, the keywords are case-insensitive, but they are most readable when shown in the MixedCase form that used to be required. Values can be separated by any number of spaces or tabs.

The properties file can have comments starting with #.  Any line starting with # will be ignored.  A property containing numeric entries can have a comment after the numbers.  However, a property specifying a general string entry (for example, any path entry) cannot have a comment on the same line beause it will be considered part of the entry.

General entries
General camera control properties
GIF properties
Properties for one camera
File options
Microscope properties
Autofocus, autotuning, and autoalignment properties
Task and montage operation properties
Tilt Series Controller properties
Navigator properties
Beam intensity calibration properties
JEOL properties
Hitachi properties
STEM properties

General entries

SerialEMProperties The file must start with this entry.
ScopeIsFEI This entry no longer has any effect.
ScopeIsJEOL This entry no longer has any effect.
UseTEMScripting On an FEI scope, set to 1 to try to create just a TEMScripting instrument object, or to -1 to try to create just a Tecnai instrument object. With the default of 0, the program will first try to create a Tecnai object then try to create a TEMScripting object if that fails. The object changed to TEMScripting in Tecnai version 3.1.1.
SimulationMode Set to 1 to indicate a microscope simulator is being used (enables some actions on JEOL and is needed to use an Eagle camera in simulation mode).
NoScope Set to 1 if there is no microscope, to avoid trying to connect with a scope.  If there is an unsupported microscope, this can be set to the KV of the microscope to get rings and a defocus value when clicking on an FFT.
GainReferencePath The path to SerialEM's gain references, if it is not the system path.
MRCHeaderTitle Title to be placed in MRC files; full title is SERIALEM: 'your title' date-time . Your title is limited to 45 characters
LogBookPathName Full path name of a text file in which tilt series information will be logged. The 'log book' contains tab-separated entries as follows: Date/time, image filename, starting Z value of tilt series, total number of Z values in the file, full image X size, Y size, file size in MB, starting angle, ending angle, tilt increment, COS for cosine increments or REG if not, minutes for tilt series, frames for montage or 1x1 for single-frame, camera name, nominal film mag, binning, pixel size in nm, LD for lowdose or ND if not, slit width if filtered or 0 if not, energy loss or 0 if not filtered.
PluginPath Alternative path from which to load plugins; the default path 'C:\Program Files\SerialEM\Plugins' is not searched.
StartupMessage This entry can be added to provide a message upon program startup. The entry must be all one line but the message can consist of multiple lines, separated by \n. The message is printed to the log window if it is reopened, otherwise to a message box.
PrintStartupInfo Set to 0 to stop program version, build time, and startup time information from being printed in the log window if it is open.
WarnIfKVnotAt Use this entry with a KV value (e.g., 200) to get a warning message box if the program is started with the microscope at a different voltage.
ControlSetName # name Use this entry to rename one of the camera control sets. Follow with the index (between 0 and 6; 0 to 4 are View to Preview) and the new name. The new name may not be substituted in all dialogs and message boxes and it may not all appear in a dialog if it is much longer than the name that it is replacing.
SearchAreaName Use this entry to rename the Search area in Low Dose mode.
DisplayIsNot120DPI The program detects the display resolution (DPI, dots per inch) when it starts and by default it modifies font sizes and some constants if it is not 120 DPI.  Set this property to 0 to use the default font sizes and dialog scalings even if the detected DPI is different from 120.  Set it to 1 if the detected DPI is 120 and you enter a different value in the 'AssumeDPI'  property, so that both dialog and font scaling will occur.
AssumeDPI Follow with a DPI value to use in font and dialog scaling instead of the detected one, see previous property.
PanelConstants Follow with three numbers: the height of the title bar to assume when floating a control panel; the extra height to add to control panels; and the extra width to add to control panels.  The defaults are 24, 5, and 8 for DPI < 120, 24, 0, and 0 for DPI = 120, and
40, 6, and 10 for DPI > 120.
ExitOnBadScopeStartup Set this to 1 to have the program exit if errors occur when connecting to the microscope.
StartAsAdministrator Set to 1 to turn on Administrator mode when starting the program.
IgnoreShortTermCals Set to 1 to prevent the program from reading in "Short term calibrations" when starting and from saving them when exiting. This might be useful when first setting up the program if there are troubles with image shift calibrations.
MaxStackWindowSizeXY This setting controls the maximum size of binned images that will be displayed in a separate window during a tilt series. Enter the maximum size for a square image; rectangular images will be binned to have no more pixels than a square image of this size. The default is 512.
TotalMemoryLimitMB Limit on the total memory that the program should use for image buffers and camera reference images, in megabytes. This limit is applied when the program is requesting memory for a montage overview image, acquisition image, or display buffer, the situations where the largest images can get created.  If the computer has 2 GB or memory or less, set this to the highest amount of memory that the program can comfortably use without causing swapping (e.g., perhaps 1200 for a 1.5 GB system). For a 3 GB system or a 4 GB system without the /3GB boot parameter, a value near 1900 might be appropriate to keep the program from running into the 2 GB memory limit. For a 4 GB system with the /3GB boot option set, this entry may not be needed, but 2700 would probably be a good value.
SkipGainRefWarning Set to 1 to suppress the warning that the spot was normalized before starting to take a gain reference. This may be appropriate on a Tecnai F30.
FFTCircleRadii Enter one or more values to customize the circles that can be drawn on a live FFT. The radius is expressed as fraction of the distance from the center to the edge of the FFT (Nyquist frequency). The default is one circle at 0.33.
FFTZeroParams Parameters governing the display of circles at the expected zeros of the CTF when a point is clicked in an FFT.  See FFT command help for details.  For with 1, 2, or 3 values: the spherical aberration in mm, the number of circles to draw, and the amplitude contrast ratio (defaults 2, 5, and 0.07).
GridLinesPerMM Number of lines per mm in the cross-line replica grating being used to calibrate pixel sizes. The default is 2160.
CatalaseAxisLengths Distances along the short and long axes to assume for catalase crystal when finding pixel size.  The defaults are 6.85 and 8.75.
SMTPServer Name of an SMTP server (of the form 'machine.domain.edu') that will accept and deliver email from SerialEM. To send email, this property and 'SendMailFrom' must be defined and an address to send to must be entered with 'Set Email Address' in the Tilt Series menu. There is a script command, 'SendEmail', that can be used to test this capability.
SMTPPort Port to use for sending to the SMTP server; a default port will be used if this is not specified
SendMailFrom Sending address to use in emails, which can be in two forms: fixed_name@machine.domain.edu or just machine.domain.edu. In the first case emails for all users will come from the same name (which could be SerialEM); in the second case the user's name will be added to the sending address, so that it will appear to come from you. The address probably needs to look like a valid address but does not need to be valid.
SocketServerIP Socket ID and IP address of a server that SerialEM will connect to through its socket interface.   The ID is an arbitrary positive number specific to a type of server.  ID 0 is assigned to the interface to the SerialEMCCD plugin (so 'SocketServerIP 0 x.x.x.x' has the same effect as 'GatanServerIP x.x.x.x') and ID 1 is assigned to the interface in the FEIScopePlugin that connects with a server on an FEI scope.  Thus, use 'SocketServer 1 x.x.x.x' to connect with an FEI scope through that server.  ID 4 is assigned to JEOL camera server, 5 is assigned to the Tietz camera remote server, and 6 is assigned to the Hitachi remote shared memory server.
SocketServerPort Socket ID and port number for a server whose address is given in a 'SocketServerIP' entry.
SocketServerIPif64 Socket ID and IP address of a server to be used only if running a 64-bit version; be sure to enter the port with SocketServerPortIf64 and not with SocketServerPort.
SocketServerPortIf64 Socket ID and port number of a server to be used only if running a 64-bit version.
BackgroundSocketToFEI Set to 1 to open a fourth socket connection to an FEI scope for tilting slowly while acquiring data.
SmallFontsBad This entry now has no effect.
SingleTecnaiObject This entry is disabled
DebugOutput

Set to 1 to obtain general debugging output in the Log Window. Set to a list of key letters (e.g., JTC) to obtain additional output corresponding to the particular key letters. Key letters are:
A to autosave log on debug output (save file must already be defined)
B for beam blanking
C for focus calibration derivation
D for  Direct Electron camera
E for eagle camera
G for verbose GIF and magnification lookups (during JEOL updates)
H for Hitachi
I (upper case i) for intensity changes in state changes/autocentering
J for complete listing of JEOL calls
K for socket interface
L for more verbose low dose
M for Moran montaging time stamps
R for camera retraction
S for stage and montaging information
T for Tietz setup/reset time, camera coords, auotoalign time
V for vacuum gauge status output
W for Winkler's bug/autoloader
a for alignment correlation coefficients
b for beam shift
c for calibration and scale matrix derivation
d for reason why no electron dose
e for JEOL event reports
f for STEM autofocus
g for GIF and STEM state setting/tracking
h for navHelper
i for image shift-related items
j for JEOL camera
k for keystrokes
l (lower case L) for low dose
m to output all SEMMessageBox messages to log
n for Navigator map transform and other items
p for AlignWithScaling and FindBeamCenter output
r for gain and dark references
s for STEM in general
t for exposure time changes in tasks and for continuous mode timing
u for update items when polling
y for reports when background saving starts and ends

ExitWithUnsavedLog Set to 1 to prevent being asked whether to save log before exiting.
ContinuousSaveLog Set to 1 to turn on continuous saving of the log.  Use this if the program is crashing on startup and a crash log is not being saved; it will ask for a log filename on the first trace output and all log output will go into the file after that.
TestGainFactors Set to 1 to multiply simulation images by gain factors.
NoExceptionHandler By default, the program will intercept crashes and attempt to close valves or turn off the beam immediately if the user's settings specify that this should occur when a message box has been up for a period of time; and will then try to save the log.  Set this to 1 to not set up the unhandled exception handler for this; or -1 to skip the Microsoft error  report box that comes up after SerialEM's message box.

General camera control properties

(These properties are all entered outside of 'CameraProperties' sections for individual cameras.)

NumberOfCameras This property has been discontinued.
ActiveCameraList A list of all of the camera numbers for cameras that are active.  Any Gatan cameras in this list must be in the same order here as the order in which they appear in DigitalMicrograph. The camera numbers can be from 0 to 5 and correspond to the numbers on the 'CameraProperties' lines.
GatanServerIP IP address for connecting with DigitalMicrograph through a socket interface instead of with COM.  This can be either the IP addess of a remote computer or 127.0.0.1 for the computer running SerialEM.
GatanServerPort Port number for the socket connection to the Gatan server.  Any free port above 1024 can be used, 48890 is suggested.  An environment variable, SERIALEMCCD_PORT, must be defined with this port number on the computer running DM.
IgnoreGatanCameras A list of Gatan camera numbers to ignore out of the cameras identified by DigitalMicrograph, numbered from 0.  For example, if DM identifies 3 cameras and you want SerialEM to access only the second one, enter '0 2'.  This list applied only to cameras accessed via a COM interface.
IgnoreSocketCameras A list of Gatan camera numbers to ignore out of the cameras identified by DigitalMicrograph accessed as a socket server, numbered from 0.
IgnoreAMTCameras A list of AMT camera numbers to ignore out of the cameras identified by the AMT software, numbered from 0. 
OtherCamerasInTIA Set to 1 if only one FEI camera is listed in these properties, but the microscope user interface allows selection of more than one camera.  With this option, the program will allow you to reselect the listed camera in the microscope interface and use it from SerialEM.
InitialCurrentCamera The index on the CameraProperties line of the camera that should initially be set as the current camera. Without this entry, the program will start with the first camera in the active camera list, or the first nonGIF camera if that is a GIF camera.
KeepEFTEMstate Set to 1 to avoid switching between EFTEM and normal lens mode when starting or exiting the program.  If 'InitialCurrentCamera' is not set, then it will stay in the current state and pick an initial camera appropiate for that state.  If 'InitialCurrentCamera' is set, it overrides this entry on program startup.  In either case, the program will stay in EFTEM when exiting.
DefaultGIFCamera The position in the ActiveCameraList (numbered from 0) of the camera that should be selected when entering EFTEM mode.  If this is not set, the first GIF camera in the list will be used.
DefaultRegularCamera The position in the ActiveCameraList (numbered from 0) of the camera that should be selected when leaving EFTEM mode or STEM mode.  If this is not set, the first regular camera in the list will be used.
GainNormalizeInSerialEM 1 to perform gain normalization and dark subtraction in SerialEM or 0 to have all processing done in DigitalMicrograph or TIA. This is an initial, global setting that will be overridden by a setting for NormalizeInSerialEM in a specific camera's properties. It can also be changed by the user on each instance of the program.
SeparateGainReferenceKVs A list of KV values at which the program will automatically maintain a separate gain reference; e.g., '80 120' for a 200 KV scope. When the scope is close to one of these values, the program will attempt to access a gain reference file specific to that KV for gain normalization, and a new gain reference will be stored in a file specific to that KV. In addition, the program will not fall back to a DigitalMicrograph gain reference in the absence of a SerialEM reference. Do not include the standard operating KV of the scope in this list.
ReferenceMemoryLimitMB The total memory allocated for dark references in SerialEM. Needs to be large for a 4K camera, e.g., 160 MB.
DarkRefAgeLimit When gain normalization is done in SerialEM, a new dark reference will be taken if one is older than this time, in seconds.
GainRefInactivityLimit When gain normalization is done in SerialEM, SerialEM will examine whether there is a new gain reference in DM if no image has been taken for longer than the given number in seconds. If DM gain references are being used, the new one will be fetched; if SerialEM gain references are being used, the user will be asked whether to use the newer one from DM instead. This number should be set a little less than the shortest reasonable time that it would for a user to switch to DM and take a gain reference.
DigitalMicrographReferencePath The path to the folder where DM keeps gain references.
RemoteDMReferencePath The path to the folder where DM keeps gain references on a remote socket-based server.  If a remote server is used, this path is needed for monitoring DM references there, unless it is the same as the 'DigitalMicrographReferencePath' entry, which is used if this path is not entered.
InnerXRayBorderDistance When removing X-rays from a dark reference, the mean of surrounding pixels will be computed from pixels that are at least this distance from all pixels above the criterion (default 1.2).
OuterXRayBorderDistance Pixels will be used to compute mean of surrounding pixels if they are no more than this distance from a pixel above the criterion (default 2.1).
XRayCriterionIterations If a patch of points above the basic criterion is too big, then criterion will be raised for up to this many iterations to try to get the brightest subset (default 3).
XRayCriterionIncrease On each such iteration, the criterion applied is the basic criterion times (1 + iteration number x this value).  Default is 1.
GlobalExtraRotation The angle to add to the rotation angle reported by an FEI scope (or more generally, the rotation angle in the magnification table), to get the actual image rotation, i.e., the rotation of the tilt axis from the X axis.
RetractCameraOnEnteringEFTEM 1 to have an upper camera retract and the beam blanked during the retraction when EFTEM mode is turned on. This is necessary only if there is a pressure switch overriding the GIF's blanking of the beam, because there is a delay between the time when the upper camera unblanks the beam and the time when the pressure switch allows the GIF to blank it again.
BlankWhenRetractingCamera 1 to have the beam blanked whenever any camera is retracted to unblock the path to a lower camera.
DefaultActAfterExposures Set the starting or default value for the Post-actions setting that allows tilting and image shift to start during camera readout; i.e., 0 to disable post-exposure actions until the user enables them.
DefaultCameraDivide16BitBy2 Set to 1 to have all images from 16-bit cameras divided by 2 as they acquired in SerialEM. This is a default behavior that can be changed by each user.
UnsignedTruncationLimit Sets the maximum fraction of pixels that can be truncating when saving unsigned data to a signed integer file; an error is generated when this fraction is exceeded.  The default is 0.01.
MinimumBlankingTime The time that it takes to blank and unblank the beam, measured by the Camera Timing Calibration routine. This entry is needed if there is a Gatan camera with two shutters, and for measuring STEM flyback times.
StartCameraInDebugMode 1 to turn on debug mode as soon as the connection to the camera is initialized. This will print all communication with the camera plugin to the DM Results window and also provide some verbose output to the SerialEM Log Window.
TietzFilmShutterSwitchTime Seconds to wait after switching the Tietz camera to film shutter mode; this time specifies the minimum pre-exposure time that will occur on the first acquisition after switching to film shutter.
CameraTimeoutFactor Factor by which to increase the time allowed for image acquisition before a timeout occurs. The default timeout is 5 seconds plus pre-exposure/exposure time plus readout time estimated from a readout rate of 0.15 megapixels/second.
CameraRetries Number of times to retry taking an image when a camera timeout occurs.  Do not use this property except to find out if retrying will overcome the original problem.
MakeFEIerrorBeTimeout Set to 1 to convert a COM error from an FEI or Gatan camera into a timeout. (Yes, the same property works for Gatan cameras).  Use this together with CameraRetries to see if trying again will overcome the original problem; use CameraTimeoutFactor with a number greater than 1 to increase the time delay between the retries.
DarkRefMaxMeanOrSD Maximum mean or SD value allowed for a dark reference, if a positive number is entered for either.  If the mean or SD of the central 80% of a dark reference exceed one of these criteria, the reference will be retaken up to two times after toggling the beam blanker.  Using the mean may be problematic so the safest entry may be 0 and a maximum SD.
OneViewMinExposures Minimum exposure times for OneView camera at each binning, in seconds.  The defaults are 0.04, 0.01, 0.005, 0.005.
OneViewDeltaExposures Allowed increment in exposure times for OneView camera at each binning, in seconds.  The defaults are 0.01, 0.01, 0.005, 0.005.  Except for binning 1, these correspond to the times allowed in the basic user interface in DM.  Increments of 0.001 appear to work for all binnings but may not be supported by Gatan over time.
SmoothFocusExtraTime Set the extra time in millisec for the focus ramp activated by the script command SmoothFocusNextShot.  The ramp will start prior to the expected start of the exposure by half of this value.  The default is 400.
K2 General Properties  
ScalingForK2Counts A scaling factor to be applied to images from the K2 camera in counting and super-resolution modes.  This can be set to make the counts match those in linear mode in the middle of the range of useful dose rates for counting mode.  If this property is not entered, the CountsPerElectron is used to scale counts, but this will make the modes match only at very low dose rates. Do not set this property to 1. Follow the instructions in Measuring Camera Gain
K2FilterName The name of one filter that can be used for aligning K2 camera images in Dose Fractionation mode.  The name must exactly match the name in DM, including '(Default)' if present, or DM may crash if the filter is used.
NoK2SaveFolderBrowse If the K2 camera is on another computer and there are no shared filesystems accessible from the both that computer and the one running SerialEM, set this to 1 to suppress the 'Browse' button that appears in the dialog for entering the folder to save frames into.
MinimumK2FrameTime Minimum duration for a frame in Dose Fractionation mode on the K2 camera.  The default is 0.025 sec if K2Type is 1 (for a K2 Summit camera) or 0.1138 sec if K2Type is 2 (for a K2 Base camera, or Summit in Base mode).
K2ReadoutInterval Value which exposure time is constrained to be a multiple of in Linear mode on the K2 camera.  The default is 0.0025 sec if K2Type is 1 (for a K2 Summit camera) or 0.1138 sec if K2Type is 2 (for a K2 Base camera, or Summit in Base mode).
K2BaseModeScaling Scaling that the SerialEMCCD plugin will apply to images if K2Type is 2 (for a K2 Base camera, or Summit in Base mode).  The default is 0.25.
K2PackRawFramesDefault Sets the default for how dose fractionation images taken without software gain normalization are saved: 0 for their original form, short integers for counting mode and bytes for super-resolution mode, or 1 for a packed form, bytes for counting mode and 4-bit data packed into bytes for super-resolution mode.  This default is overridden by the user's setting, if it exists.
K2SynchronousSaving Set to 1 to save dose fractionation images after the stack is fully prepared, i.e., synchronously.  The default is to save asynchronously, as soon as each image in the stack becomes available.
K2MaxRamStackGB Maximum number of GB available for keeping dose-fractionation frames in memory, including frames held within DM and within the SerialEMCCD plugin.  This setting is relevant for GMS 2.31 and above.  The default is 12.
K2CountingReference Full path and name of counting mode software gain reference on the K2 computer, so that the reference can be saved along with data when taking dose fractionation images without gain normalization in counting mode.  This property and the next one are no longer needed for a standard arrangement; if one of these properties is absent, the name is composed from the appropriate DM reference path property and the property 'DMGainReferenceName' for the particular camera.
K2SuperResReference Full path and name of super-resolution mode software gain reference on the K2 computer, so that the reference can be saved along with data when taking dose fractionation images without gain normalization in super-resolution mode.
K2MinStartupDelay Minimum StartupDelay for a K2 Summit camera in seconds; post-exposure actions will not be allowed if the StartupDelay property is less than this value.  The default is 3.0.
CalibTimingK2InitialStartup Initial startup delay time when calibrating camera timing with a K2 Summit camera, in seconds.  The default is 2.
Falcon General Properties  
FalconReadoutInterval Value which intermediate frames are constrained to be a multiple of with Falcon camera.  The default is 0.055771 sec, which works for a camera that reads out at 17.9 FPS.  It needs to be set to 0.058824 for a camera that reads out at 17 FPS.
MaxFalconFrames Maximum number of intermediate frames that can be saved for Falcon 2 with old scripting interface.
FalconFrameConfigFile Full path and name of the configuration file that controls the saving of intermediate frames for Falcon 2 with old scripting interface.
FalconConfigFile Full path and name of FalconConfig.xml file that contains an entry for whether intermediate frame saving is turned on.  By default,the program will look in the same directory as the file specified with 'FalconFrameConfigFile', so this entry is not needed unless these files are in different directories.
SetModeInFalconConfig Set to 1 or 0 if the intermediate frame saving mode can or cannot be controlled solely by modifying FalconConfig.xml.  By default, the program assumes that editing this file is ineffective if the file contains text like '<FrameProcProgName>Mode_4' and is effective if the text is like 'AcquisitionMode="Normal"', so this entry can be used to override that assumption.
LocalFalconFramePath For Falcon 2 with old scripting interface, path to directory where intermediate frames should always be written initially .  If this is not entered, frames will be written to whatever folder is chosen by the user.   A local path should be supplied if users can choose remote directories that FEI software will not write to.  For Falcon 2 with new interface or Falcon 3, path to top directory where frames are written by the FEI software, as seen from the computer running SerialEM.  For Falcon 2, this is needed to enable saving command files for aligning in IMOD, and only when SerialEM is not running on the microscope computer. For Falcon 3, it is needed regardless of where SerialEM is running to enable aligning of frames in SerialEM or IMOD. (If SerialEM is running on the Falcon 3 storage server, this entry would typically be  'C:\OffloadData\TemScripting\BM-Falcon'
FrameMdocForFalcon Set to 1 or 2 to save metadata into a file opened with Open .mdoc for Frames in the File menu for Record images or all images from a Falcon camera, respectively.  Use this property to get metadata saved when you are capturing frames from Falcon acquisitions by connecting to the internal transfer of frame data.
FalconPostMagDelay Delay in milliseconds for taking an image from a Falcon camera after a magnification change.  This delay may be needed to keep the Dose Protector from blocking the shot because of transient conditions associated with the mag change.  The default is 10 (effectively disabled).
DE General Properties  
DEProtectionCoverOpen Set to 1 to have the program start with the protection cover mode set to being open during operation for a Direct Electron camera; the default is for it to open and close for each single exposure, and be kept open during tasks.
DEProtectionCoverDelay Set to a delay for the protection cover opening, in msec.  If this property is not entered, the delay value will come from the last value set in the server each time that SerialEM starts.
DETemperatureSetpoint Set to the desired temperature setpoint for a Direct Electron camera.  It is recommended that this property not be entered and that the setpoint be set in the server configuration instead.

Energy filter properties

BiggestGIFApertureNumber The number of the aperture that must be in place for imaging. You could image an aperture by entering its number here.
MinLowMagSlitWidth Minimum slit width when doing low mag tasks (default 25).
SlitWideningSafetyFactor When doing a low mag task, the slit will be opened if necessary to the minimum slit width, and intensity will be reduced by the ratio of original to new slit width times this additional safety factor (default 0.75).
FilterPixelMatchingFactor Factor by which to multiply the actual, calibrated pixel size on the GIF camera when matching pixel size upon a mag change. This can be used to match field of view instead of pixel size for two cameras with different CCD sizes; e.g. one would use a value of 2 with a 1K 794 before the GIF and a 2K 795 GIF camera. It can also be used to compensate for a difference in the binning definitions of the two cameras with similar CCD size; e.g., use a value of 0.5 if there is 4K, 15-micron pixel camera before the GIF and a 2K, 30-micron pixel GIF camera.
FilterSlitInOutDelay Delay time in DM ticks (60th of second) with a GIF, or in msec with an omega filter, when inserting or retracting slit.  Default is 18.
FilterOffsetDelayCriterion For filter offset changes less or more than the criterion, delay time in ticks is computed as change * slope1 + base1 or change * slope2 + base2, respectively.  Default is 40.
FilterOffsetDelayBase1 Base delay (in ticks for GIF, msec for Omega filter) for offsets less than the criterion. Default is 10.
FilterOffsetDelaySlope1 Additional delay per EV of offset for offsets less than the criterion.  Default is 0.5.
FilterOffsetDelayBase2 Base delay (in ticks for GIF, msec for Omega filter)) for offsets greater than the criterion.  Default is 30.
FilterOffsetDelaySlope2 Additional delay per EV of offset for offsets greater than the criterion.  Default is 0.25.
NoSpectrumOffset Set to 1 to indicate that Spectrum Offset cannot be set and Energy Shift should be set instead.  This is generally needed on JEOLs, and is needed with a Quantum Life Science energy filter that lacks spectroscopy mode.
MaximumSlitWidth For a GIF,  set the maximum slit width available.  The default is 50 eV.
GIFadjustsForSlitWidth Set to 1 if DM adjusts the GIF settings for changes in slit width so as to keep the ZLP in the middle of the slit.  By default, SerialEM assumes that it needs to account for slit width changes in the 'Adjustments' shown in the Filter Control panel.  To see if this setting is needed, align the ZLP with a slit width of 20 and see if the image is lost as the slit width is stepped below 10 eV.
DMAlignZLPCriteria Set the criteria for detecting whether the ZLP is being aligned in DigitalMicrograph.  Follow with one or two numbers; the first is the number of energy shift changes over which it will look at the time interval between changes, the second is the maximum time interval between those changes in order for a Align ZLP to be assumed.  The defaults are 3 and 6., which means that the program needs to see 3 changes within 6 seconds to detect the Align ZLP.  Turn on Debug Mode in the Camera menu to see what changes it detects and their intervals.  Only one of the several '3-change times' needs to be reliably less than the maximum time interval set here.
AllowSpectroscopyImages Set to 1 to allow images to be taken in spectroscopy mode.

Properties for one camera

(all times are in seconds)

(These properties are all entered inside of a 'CameraProperties' sections for an individual camera.)

(For a Tietz camera, StartupDelay, MinimumDriftSettling and ExtraBeamTime are the only timing parameters that are relevant, and any other property that refers specifically to Gatan camera or DigitalMicrograph (DM) is not relevant.)

CameraProperties This entry, followed by a camera number from 0 to 3, signals the
start of a section of properties for a camera, which can include any of the entries in this table.
Name The name of the camera, which will appear in the camera, montaging, and tilt series setup dialogs. Spaces are allowed.  For an FEI camera, a required name must be entered here unless it is entered with 'DetectorName'.
DetectorName Use this entry to indicate the required name for an FEI CCD camera, if it is different from the entry given by 'Name'.  Follow with 0 and the name.  The name must be 'CCD' for Tecnai versions before 4.1, and names like 'BM-Eagle' and 'BM-Falcon' thereafter.
UseSocket For a Gatan camera, set to 1 to connect with this camera through a socket instead of COM interface.
TietzCameraType 0 for a non-Tietz camera
1 for Tietz simulation camera
2 for PXL camera (older F214, F224 with the PXL controller)
3 for PVCam camera (older Tem-Cam-F0124, F214 with the Model 300 controller from Photometrics, also some 4k F415MP multi-port readout)
4 for FastScan F114 camera using MVTitan PCI frame grabber
5 for SCX camera (F224HD, single-port F415 with SCX controller)
6 for FastScan F114 camera using FireWire 1394 interface
7 for ATC6 camera (very old F224)
8 for old TemCam-F816 with Firewire controller, 9 for TemCam-F415MP (4k camera with multi port readout), 10 for FastScan-F214 with Firewire controller, 11 for TemCam-F416
12 for TemCam-F216
13 for new TemCam-F816
Entries of 8, 11, 12, and 13 imply a RestrictedSizeType of 4. For these cameras, make CameraSizeX and Y be the full size of 8200, 4100, or 2050, respectively, not 8192, 4096, or 2048.
AMTcameraType 1 for an AMT camera. AMT cameras can coexist with Gatan cameras after SerialEM 3.2.3.
FEIcameraType 1 for an FEI Eagle camera or FEI STEM, 2 for a Falcon 1 or 2 camera, 3 for Ceta 1 or 2 or another camera with no shuttering capabilities, or 4 for Falcon 3.  If the type is 2 and a camera is determined to have electron counting and aligning capabilities, it will be converted to a 4. This entry implies RestrictedSizeType 1. It also implies a MinimumExposure of 0.011, unless a different value is entered, or unless the new FEI camera interface is available.  12 and 14 can be used to test various features for Falcon 2 or 3 with the new interface even when it is not present.
DEcameraType 0 for a non-Direct Electron camera, 1 for a 4K LC1100, 2 for a DE12, DE16, DE20, or DE64, 3 for a DE12/16/20/64 Survey camera, or 4 for a DE_LC1100.  This entry implies RestrictedSizeType 3 for the LC1100 only.
K2Type Set to 1 for a Gatan K2 Summit camera or 2 for a Base camera or for a Summit booted into Base mode.
OneViewType Set to 1 for a OneView camera.
RotationAndFlip This entry is used for STEM cameras and K2 and Falcon cameras. For a STEM camera, use it to indicate whether to rotate and flip images after acquisition to make them match image orientation on the screen and other cameras.  The value is the sum of 0-3 for the number of 90 degree rotations counterclockwise (e.g., 3 for 90 degrees clockwise) plus 4 for flipping around the Y axis before the rotation.  Set this before doing any calibrations that rely on image orientation. For a K2 camera, this entry indicates operations to be applied to dose fractionation images returned to SerialEM and to frames saved from the plugin by default.  Even if frames are being saved without rotation and flip, the correct entry is needed here to keep DM from applying its own rotation.  For a Falcon camera, the indicated operation is applied to intermediate frames.
DMRotationAndFlip This entry can be used for any Gatan camera to indicate the setting for rotation and flipping around the Y axis in the camera configuration in DM.  The value to enter is the rotation in the camera configuration divided by 90 (i.e., 0-3) plus 4 if there is flipping around the Y axis.  By default, the program will set the camera to this configuration at startup and restore the original configuration when it exits, issuing a warning in the log.
SetRestoreDMRotFlip Use this entry to control what happens when a Gatan camera's configuration does not match the value in 'DMRotationAndFlip'.  Enter 0 to have it ask whether to change the configuration, or 1 to have it set the configuration automatically but not change it back upon exit.
AlignedSumRotFlip Use this entry for a Falcon camera to specify the rotation and flip operations to apply to the summed image after aligning frames in SerialEM.  The value is the same as what could be specified in 'RotationAndFlip', and this entry is not needed if 'RotationAndFlip' is entered.  It would be used if 'RotationAndFlip' is omitted in order to save time when saving frames.
UseContinuousMode The entry can enable use of a fast continuous acquisition mode for a Gatan or Direct Electron camera where this mode is not enabled by default, or to modify or disable use of the mode if default parameters are available.  For a Gatan camera, follow with up to 4 numbers: 1 to use the mode or 0 not to; 1 to specify continuous readout or 0 not to; a quality level from 1 to 7 or 0 not to set quality; and 1 to balance intensity between two halves of the field.  If no property is entered, the defaults are '1 1 1 1' for Orius cameras, '1 1 0 0' for K2, and '1 0 0 0' for US4000 and US1000 cameras, where the camera type is determined from the 'DMGainReferenceName' property.  If a property is entered for an Orius, be sure to include the fourth value to balance the two halves, unless using a quality level where it is not needed.  For a DE camera, the use of live mode is specified by the first parameter, and the use of a separate thread that acquires in parallel with the display operations is specified by the second parameter; both values are set to 1 by default.
BoundaryBetweenHalves Specifies the location and orientation of the boundary when balancing intensity between two halves in continuous mode.  By default, the boundary is assumed to be at the midpoint, and the orientation is determined by querying DM for the image orientation.  Enter the unbinned pixel just above the boundary (numbered from 0) and optionally, enter 0 if the boundary is vertical or 1 if it is horizontal.
RestrictedSizeType Set to 1 if acquisitions are restricted to full, half and quarter centered images. Set to 2 if subarea acquisitions simply do not work; this will set SubareasAreBad to 2. Set to 3 if subareas must be centered. Set to 4 for Tietz cameras with 1024-block readout on 1025-pixel boundaries. Set to 8 for DigiScan.
TaskTargetSize Target size to bin to for task images.  Trial parameters are used as a basis, and binning is increased if necessary to make the image no bigger than the target size, with exposure time reduced to compensate. (This is not done for K2 cameras). The default is 512.  Set this higher for a specific camera to allow less binned images to be used.
TietzCanPreExpose Set this entry to 0 or 1 to indicate whether a Tietz camera has a shuttering mode that allows pre-exposure of the specimen, using the film shutter and beam blanker. This setting works only if the EMShutter module is installed and an appropriate Tietz shutterbox is being used.
TietzGainIndex Gain index to use for a Tietz camera. This is not the gain itself but a number between 1 and the number of gains available. The default is 1.
TietzImageGeometry Sum of values to flip or rotate image from Tietz camera: 1 to mirror on X axis, 2 to mirror on Y axis, 4, 8, or 16 to rotate 90, 180, or 270 degrees counterclockwise.
DMGainReferenceName The full name of this camera's DM gain reference, including spaces and .dm3 or .dm4.
CameraSizeX Number of pixels in X.
CameraSizeY Number of pixels in Y
XMustBeMultipleOf This entry constrains the size in X of images to be acquired to be a multiple of the given number. This entry is overridden by a RestrictedSizeType entry. This entry probably needs to be at least 2 because of some problems with image display.
YMustBeMultipleOf This entry constrains the size in Y of images to be acquired to be a multiple of the given number. This entry is overridden by a RestrictedSizeType entry.
CoordsMustBeMultiple Set this entry to 1 if the individual coordinates (left and right in X, top and bottom in Y) must also be a multiple of the values specified in XmustBeMultipleOf and YmustBeMultipleOf, respectively.
GainRefXsizeEven Set this entry to 1 if gain references being made in SerialEM must have a size in X that is a multiple of the value entered with XmustBeMultipleOf, or to 2 if in addition, gain references from DM are even in X. The setting of 1 may be needed if there is a failure making a gain reference; 2 may be needed if errors occur with references from DM not being the expected size.
GainRefYsizeEven Set this entry to 1 if gain references must be made to have a size in Y that is a multiple of the value entered with YmustBeMultipleOf, and 2 if references from DM have an even size in Y.
SizeCheckSwapped Set this entry to 1 if the X and Y sizes reported by a Tietz camera need to be swapped when checking camera size, or to -1 to skip the size check for a Gatan or Tietz camera.  It is no longer needed for a Gatan camera where X and Y are swapped from their native sizes.
HalfSizes For an FEI camera (or camera of restructed size type 1), if the camera size does not divide evenly by subarea size and binning, this entry and the next can be used to enter the actual acquired image sizes at each binning.  Enter the X and Y size of a center-half image at each binning (X at 1, Y at 1, X at 2, Y at 2, etc).
QuarterSizes Similiarly to HalfSizes, enter the Xand Y size of a center-quarter image at each binning.
FourPortReadout Set this entry to 1 for a 4-port readout camera.
BasicCorrections This entry determines the corrections done for all image acquisitions in DigitalMicrograph. It can be the sum of 1 for defect correction, 16 for bias correction, and 32 for linearization. The default value if none is entered is -1, which means that default corrections will be done for the particular camera.
MakesUnsignedImages Set this entry to 1 for a 16-bit camera that produces unsigned 16-bit integer images.
CountsPerElectron The camera gain, i.e. the number of counts per primary electron. This entry is needed for dose estimates. It should be in counts before dividing by 2 for a 16-bit camera.  For a K2 camera, set to the number of linear mode counts per electron, not to a value near 1.
Binnings A list of valid binnings for this camera. Up to 9 binnings may be listed and will appear in the camera setup dialog.
BinningOffset This entry may be needed to make gain normalization work well in binned images when gain normalization is being done in SerialEM. Follow the keyword with 4 numbers: the binning of images being normalized, the binning of the gain reference (1 or 2), the offset in X (a small positive or negative number), and the offset in Y. Offsets may be needed for Tietz and Eagle cameras. The appropriate offsets will be set up automatically for 4-port readout cameras for binnings that are not a power of 2, but these entries could be used to override the assumed settings. To prevent the binned by 2 reference from being used with a higher even binning, enter a line with 'binning 2 999 999'.
RelativeGainFactors A list of relative camera gain values, one per binning listed on the Binnings line. This entry is needed for the Eagle and some other FEI cameras, OneView camera, Tietz CMOS cameras, and for DE cameras configured to bin by averaging instead of summation. The factor should be 1 for the binning at which counts per electron is calibrated.
AutoGainFactors The binning index at which to start applying an automatically set gain factor, for an FEI camera with the advanced scripting interface.  With a value of 1, binning will essentially average instead of summing values, so counts are scaled by 0.25 , 0.0625, and 0.0156 at binnings 2, 4, and 8.  With a value of 2, the scalings would be 1, 0.25, and 0.0625 at 2,  4, and 8.
ExtraGainReferences Enter the number of binnings above 2 for which to allow separate gain references to be acquired. Up to 6 additional gain references may be saved, for the six binnings following 2 on the 'Binnings' line. These references may be useful if there are problems with quadrant correction on four-port cameras and if the imbalance between quadrants differs between binnings. They may also be needed if binning 1 is unusable.
NormalizeInSerialEM Initial setting (0 or 1) for whether images should be gain-normalized in SerialEM. A value for a specific camera overrides the global default value provided by GainNormalizeInSeriaEM.
UsableArea Specifies the coordinates of the usable area on the CCD, in Digital Micrograph coordinates numbered from 0. Follow the keyword with the top, left, bottom, and right coordinates of the last good column or row on the chip. This is needed if gain normalization is being done in SerialEM.
SubareasAreBad Set this entry to 1 for a Tietz camera if taking an image of a subarea makes the next image of the full camera area, or a much larger subarea, be bad. Set it to 2 if subareas are not allowed at all. This setting affects only the image sizes used for beam intensity calibration and gain reference acquisition.
BadColumns Specify a list of bad columns that will be replaced in all processed images (gain normalized or dark subtracted). List the columns in increasing order using coordinates numbered from 0. This is needed if gain normalization is being done in SerialEM.
BadRows Specify a list of bad rows that will be replaced in all processed images.  List the rows in increasing order using coordinates numbered from 0 at the top.
PartialBadColumn Specify one or more adjacent columns needing correction over a limited extent in Y. Enter four numbers: the starting column number (numbered from 0), the number of columns, the top Y coordinate (numbered from 0 at the top of the image), and the bottom Y coordinate. Use multiple lines to enter multiple corrections.
PartialBadRow Specify one or more adjacent rows needing correction over a limited extent in X. Enter four numbers: the starting row number (numbered from 0 at the top), the number of rows, the left X coordinate (numbered from 0), and the right X coordinate.  Multiple lines can be used.
BadPixels Specify a list of single pixels needing correction.  Each pixel is specified by an X and a Y coordinate numbered from 0 at the top left.  Multiple pixels (up to 19) can be entered on one line, and anunlimited number of pixels can be entered on multiple lines.
HotPixels Specify a list of hot pixels if X ray removal from dark references is going to be used, to prevent these pixels from being treated as X rays. Each pixel is specified by an X and a Y coordinate. Multiple pixels (up to 19) can be entered on one line, and multiple lines can be entered up to 400 pixels.
HotPixelsAreImodCoords Enter 0 or 1 if hot pixel coordinates are numbered from 0 (DM coordinates) or from 1 (IMOD/3dmod coordinates) respectively.
HotColumns Specify a list of hot columns which should not be analyzed for X rays, in DM coordinates numbered from 0. Include the bad columns if they are hot.
DarkXRayAbsoluteCriterion The absolute number of counts by which a pixel must exceed the mean of a dark reference to be treated as an X ray. These should be counts before division by 2, if any, for a 16-bit camera.
DarkXRaySDCriterion The number of standard deviations above the mean that a pixel value must be to be treated as a dark reference X ray.
DarkXRayRequireBothCriteria Enter 1 if a pixel must exceed both the absolute and the standard deviation criterion to be treated as a dark reference X ray, or 0 if exceeding either criterion will do.
MaximumXRayDiameter The maximum diameter of an area that will be replaced as an X ray in a dark reference, in unbinned pixels.
ShowRemoveXRaysBox Set to 1 to enable the appearance of the 'Remove X-rays' checkbox in the camera setup dialog. This option should be enabled only if the particular camera generates images where X-rays can ruin the tracking.
BeamBlankShutter The shutter number of the beam blanking shutter (0 or 1; an FEI scope should be set up so that this is 1 when there are two shutters connected)
OnlyOneShutter Set this entry to 1 if there is only one shutter driven by this camera.  For an Eagle camera that does not work with the default 'Both' shutter setting, set to 1 to use the pre-specimen shutter or -1 to use the post-specimen shutter.
NoShutter Set this entry to 1 or 2 if the camera has no shutter, to have SerialEM keep the beam blanked when the screen is up, except when taking an image.  With a value of 1, the program will unblank before requesting an image and reblank after receiving one.  With a value of 2, it will unblank just for the exposure time in a separate thread; this can be used if the camera has predictable timing and the beam unblanking/reblanking itself does not produce image artifacts.
SetAlternateShutterNormallyClosed 1 to issue a command upon initialization to make sure that this camera is configured so that the beam shutter is normally closed and the film shutter is normally open.
BuiltInSettling The intrinsic pre-exposure time in seconds when using the regular shutter for a Gatan CCD camera; this seems to correspond to the clear time of the camera.
StartupDelay Average time in seconds between issuing a command to take a picture, and the start of the actual exposure sequence (clearing the CCD for a Gatan camera, or starting the exposure for a Tietz camera).
AllowPostActions Set to 0 to disable Post-actions (scope actions during the readout and processing time) for a camera where they are ordinarily available.  The default is 0 for a OneView camera, so enter 1 to enable post-actions for a OneView.
MinimumDriftSettling The smallest drift settling that SerialEM should try to produce. For a Gatan camera, it corresponds to half of the range of variability in the time that an exposure starts after image acquisition is requested by SerialEM. For a Tietz camera on a JEOL, this should be set to at least 0.1, or even 0.2, to prevent lower shutter exposure times less than 0.2; on an FEI scope it can be 0 or a small number like 0.01.
ExtraBeamTime The amount of time to allow after the expected end of the exposure before microscope actions can be taken and the beam can be blanked the beam to avoid beam exposure during the readout. For a Gatan camera, this should equal MinimumDriftSettling. For a Tietz camera, the sum of StartupDelay and this timing factor is used to control how soon microscope actions can be taken after readout should begin, but no beam blanking is needed.
ExtraOpenShutterTime When the shutter is opened to provide a pre-exposure that exceeds the built-in settling (pre-exposure), the time specified by this entry is subtracted from the additional pre-exposure desired to keep the pre-exposure from exceeding the desired length.
ShutterDeadTime The amount of exposure time lost when the beam shutter is operated; an entry for this is needed on JEOLs and can be obtained by running the routine in the Calibration menu.
MinimumExposure Minimum exposure time that the camera will allow.
AddToExposure Amount to add to the specified exposure time, in seconds, to get the proper exposure from the camera.  Falcon 3 initial versions needed 0.013.
PostBlankerDelay Delay in seconds between operating scripting beam blanker and taking an image.  This delay is applied in two situations: when beam is blanked before taking a dark reference, and when the beam is unblanked prior to an image, which happens after a dark reference, when in Low Dose mode, or with NoShutter set to 1.
Retractable Set to 1 to indicate that the camera is retractable
InsertionDelay Delay in seconds after inserting the camera; this delay is imposed after the camera software returns from the insertion command, so the total delay will be the sum of any intrinsic delay in the camera software and this delay.
RetractionDelay Delay in seconds after retracting the camera; this delay is imposed after the camera software returns from the retraction command, so the total delay will be the sum of any intrinsic delay in the camera software and this delay.
InsertingRetractsCam Number (camera properties index) of other camera that is automatically retracted when this one is inserted.  This property must be specificed for both cameras if the retraction works in both directions.  Using this will save the RetractionDelay time.
CheckStableTemperature Set to 1 to check for whether the camera is at a stable temperature before trying to acquire. Once the camera passes the test, the program will not check again. (For Gatan camera of controller class 'PICM', such as Orius).
SideMounted Set to 1 for a side-mounted camera above the viewing screen, so that the program will not raise the screen before taking a picture.
PixelMatchFactor This factor controls the optional magnification change to match pixel size when switching between non-GIF cameras. For example, set to 2 to have unbinned pixels in another camera matched to binned pixels when switching to this camera. The value need not be an integer.
GIF Set to 1 to indicate that this is a GIF camera
Order An arbitrary number to indicate the order of the camera in the beam path; cameras with lower order can block the beam from reaching cameras with higher order.
HasTVCamera Set to 1 to indicate that this GIF has a TV camera.
InsertTVToUnblank Set to 1 to indicate that the TV camera must be inserted to keep this camera from blanking an upper camera. This setting is needed with a GIF unless you have some other means to keep the GIF from blanking when the upper camera is in use.
FilmToCameraMagnification Magnification ratio between the film plane and the camera. This is used to provide a fallback pixel size if pixel size is neither directly calibrated nor deducible from image shift calibrations.
PixelSizeInMicrons Actual size of unbinned pixels in the CCD chip.
ExtraRotation Number that needs to be added to the rotation angle in the magnification table and the global extra rotation angle to determine image rotations for this camera. Only relevant if rotations are not calibrated directly or indirectly.
RotationAndPixel This entry specifies a set of calibration values for a single magnification. It should contain the following numbers on the line:
1) Magnification index
2) Change in image rotation from the next lower mag to this mag (in degrees, CCW positive), or 999 if this was not measured
3) The measured rotation from the X axis to the tilt axis (in degrees, CCW positive), i.e., the rotation angle solved for in Tiltalign plus 90 degrees; or 999 if this was not measured.
4) The pixel size in nanometers, or 0 if this was not measured.
SpecialRelativeRotation Relative rotation between two mags that are not adjacent. This entry will allow a rotation calibration to propagate across a gap in magnifications. Follow it with three numbers:
1) Magnification index of starting mag
2) Magnification index of ending mag
3) Rotation of image going from starting to ending mag
RotationStretchXform This entry of a linear transformation needed to align rotated images with each other allows the Align with Rotation dialog to compensate for stretch in images projected at this magnification.  See Stage and Imaging Stretch for details.
DoseRateTable Start of an alternative table for linearizing the counts in K2 or Falcon 3 electron counting images so that dose rate reports are correct.  Follow with the number of lines to follow, and an optional scaling.  Each following line should have a raw mean number of counts per unbinned pixel per second, then the corrected dose rate in electrons/unbinned pixel/sec. The raw mean counts will be divided by the scaling (1 by default), so if the mean counts are obtained from SerialEM, the scaling entered on the first line should be the scaling that was applied to the raw electron counts from DM.  The default tables in SerialEM are based on the mean of images taken in DM and the dose rate readout in DM, recorded for 200 and 300 KV.  Values are included for dose rate readouts around 1, 2, 3, 4, 6, 9, 13, 18, 26, 39, 56, 73, and 80 for 300 KV.  There is now a built-in table for Falcon 3 that was obtained at 200 KV but is applied at 300 KV also.
LinearToCountingRatio Ratio of number of counts (in SerialEM) obtained from a Falcon 3 camera in linear mode to # of counts for the same exposure in counting mode.  The counts for linear mode must be measured in SerialEM because it returns integrated rather than averaged counts.  The default is 8.
Falcon3ScalingPower This entry does two things: it enables the scaling of data from the Falcon 3 so that linear and counting modes give comparable counts for the same exposure; and it sets the number of divisions by 2 applied to the data.  If the value is 0 or negative (but greater than -10), then counting mode data will be divided by 2 the given number of times and linear mode data will be scaled to match; i.e., no division of counting mode values for 0, or division by 2, 4, 8, etc for for -1, -2, -3, etc.  If the value is positive, then linear mode counts will be divided by 2 the given number of times, i.e., by 2, 4, 8, etc. for 1, 2, 3, etc., and counting mode data will be scaled to match.  Enter -10 to disable the scaling of both kinds of data.  The default is 4, which will divide linear mode counts by 16 and scale counting mode by ~0.4 to 0.5, depending on the entry for 'LinearToCountingRatio'.
EndCameraProperties This entry indicates the end of the block of properties for a camera.
STEM camera properties  
STEMCamera Set to 1 to indicate a STEM device.  Set FeiCameraType to 1 for an FEI STEM unit; otherwise it is assumed to be a DigiScan
ChannelName Use this entry once for each detector available to this camera; this is the name that will appear in the detector selection combo boxes in the camera setup dialog.  Follow with the name of the detector.
DetectorName Use this entry to indicate the name by which a detector is accessed through FEI scripting, if it is different from the entry given by ChannelName.  Follow with the detector # (numbered from 0) and the name.  Available detector names will be printed on program startup if DebugOutput is set to 1 or any other letters.
NeedShotToInsert For an FEI, follow this with a list of the numbers (from zero) of detectors that are removed when going out of STEM and need to be inserted by taking a dummy exposure.  The HAADF detector requires this.
MinimumPixelTime Set this to the minimum allowed pixel time in microseconds.  The default is 0.1; it needs to be set to 0.5 for DigiScan.
AddedFlybackTime Set to the added flyback time indicated after running the camera timing calibration procedure.  On FEI it will be a large value that depends on the camera parameters used in the timing procedure; with DigiScan it should be small but may be needed to make acquisition times predictable enough to keep DM from crashing.
ImageRotation Set this entry to the sum of the actual rotation produced by the operation in RotationAndFlip plus 180 degrees, if necessary, to bring the tilt axis rotation angle output in the image file header to the correct value.
InvertFocusRamp Set to 1 if dynamic focus changes in the wrong direction.
MaximumScanRate Enter one or two numbers to indicate the highest scan rate that avoids distortion or excessive shift of the images.  The first number is a maximum value that will be enforced when running lower-mag tasks and applied when 'Set to Maximum Scan Rate' is pressed in the camera setup dialog.  The second number is an advisable scan rate, a lower value that might be preferable for having minimal distortion.  If only one value is entered, the maximum and advisable scan rates will be set to this value.  The camera setup dialog shows a single star after a scan rate that exceeds just the advisable rate, and three stars after a rate that exceeds the maximum.
STEMsubareaInCorner Set to 1 for FEI STEM until an FEI bug that causes subareas to be acquired in the lower right corner is fixed.  This bug is present through Tecnai 4.2 and is known to be gone in 4.6; for versions in between, experiment and let us know.
Plugin Camera Properties  
PluginName Name by which the plugin identifies itself.  When the program is started, it lists the names of loaded plugins.
PluginCameraIndex The index by which this camera is selected, if the plugin supports more than one camera.
ShutterLabel1 A label to replace the text on the first shutter radio button in the Camera Setup Dialog.
ShutterLabel2 A label to replace the text on the second shutter radio button in the Camera Setup Dialog; the line will be hidden if this entry is not made.
ShutterLabel3 A label to replace the text on the third shutter radio button in the Camera Setup Dialog; the line will be hidden if this entry is not made.  If this entry is present, ShutterLabel2 must be entered also.
PluginCanProcess Set to the sum of 1 if the plugin can return dark-subtracted images and 2 if it can return gain-normalized ones.
PluginCanPreExpose Set to 1 if the plugin can pre-expose for drift settling.
Direct Electron Cameras  
DECameraServerIP Set to the IP address of the DE server computer, or 127.0.0.1 if the server is running on the same computer as SerialEM.
DECameraReadPort Set to a port number for reading from DE server, typically 48880.
DECameraWritePort Set to a port number for rwriting to DE server, typically 48879.
DEImageRotation Set to the negative of the angle ( a multiple of 90) that the image needs to be rotated after receiving it from the DE server; i.e., 90 for clockwise and -90 or 270 for counterclockwise rotation; 180 is also allowed.
DEImageInvertXAxis Set to 1 to flip the image around the Y axis after the rotation, if any, specified by DEImageRotation.
AlsoInsertCamera Set to CameraParameterSet number of another camera that should be inserted whenever this camera is used.  The entry needs to be set for both a DE-12 and a DE-12 Survey camera.  It can be used for other camera types.
SamePhysicalCamera Set to CameraParameterSet number of another detector that is part of the same camera and thus inserts/retracts together.  The entry is needed on only one of the two cameras.  It can be used for other camera types.
DEAutosaveFolder Top folder under which frames will be saved for this camera.  This entry has an effect only with a server version of 1.0.943 or higher, where SerialEM will allow saving to subfolders of the autosave folder.  The directory will be created if it does not exist but its parent must already exist.

Obsolete camera options

CanDriveDMBeamShutter Set this entry to 0 to indicate that the installed version of DigitalMicrograph cannot drive the alternate shutter via scripting, and to override the plugin's decision based on DM version number. This should be needed only if a 3.7.1 version below 3.7.1.6 is installed.
CanUseDMOpenShutter Set this entry to 0 or 1 to indicate that extra pre-exposure (drift settling) can or cannot be achieved by the DigitalMicrograph scripting command to open the shutter. This should not be needed.
CanDriveDMDriftSettling Set this entry to 0 to indicate that the installed version of DigitalMicrograph cannot specify a DM drift settling via scripting, and to override the plugin's decision based on DM version number. This should be needed only if a 3.7.1 version below 3.7.1.6 is installed.
MinimumBlankedExposure If the beam shutter cannot be controlled through scripting in DigitalMicrograph, SerialEM must request an exposure longer than the desired one using the regular shutter and unblank the beam for the desired exposure time during this longer exposure. This entry specifies the smallest extended exposure time that will be requested.
ExtraUnblankTime When SerialEM must produce an exposure by beam unblanking as just described, this entry is needed to specify how much time to subtract from the desired exposure time to make the actual unblanked time be correct on average.

File Options

These properties determine the default options that are selected when the file properties dialog box is opened.  For two options, the default depends on whether the microscope is in STEM mode or not.

FileOptionsMode Mode for files opened when not in STEM mode: 0 for bytes, 1 for 16-bit signed integers, or 6 for 16-bit unsigned integers; the default is 1
STEMFileMode Mode for files opened when in STEM mode, 0, 1, or 6; the default is 1.
FileOptionsExtraFlags The sum of 1 to store tilt angles, 4 to store stage position * 25, 8 to store magnification / 100, 16 to store intensity * 25000, and 32 to store exposure dose.  The default is 17.
FileOptionsMaxSections Default value for the maximum number of sections, which determines the amount of space allocated for the extended header (default is 360, raised from 300 on 12/31/16).
FileOptionsPixelsTruncatedLo Number of pixels that will be truncated at 0 when scaling integers to bytes (default is 40, raised from 10 on 12/31/16).
FileOptionsPixelsTruncatedHi Number of pixels that will be truncated at 255 when scaling to bytes (default is 40, raised from 10 on 12/31/16).
FileOptionsUnsignedOption Determines how 16-bit data will be stored as signed integers for files opened when not in STEM mode: 0 to truncate at 32767, 1 to divide by 2, 2 to subtract 32768.  The default is 0 for truncation.
FileOptionsSignToUnsignOption Determines how signed data are written to an unsigned integer file: 0 to truncate negative numbers at 0, or 1 to add 32768
STEMUnsignedOption Determines how 16-bit data will be stored as signed integers for files opened when in STEM mode: 0 to truncate at 32767, 1 to divide by 2, 2 to subtract 32768.  The default is 2 to subtract 32768.
FileOptionsFileType 0 for MRC file, 1 for a series of numbered TIFF files described in an image autodoc
FileOptionsSaveMdocFile 1 to have all available information (tilt angle, magnification, etc.) saved in a metadata autodoc file, 0 not to.  This option is on by default if one of the cameras is a direct detector, in which case 0 would be needed to turn it off.
MontageAutodocOptions Set to non-zero to have the file type and metadata autodoc options be set to separate defaults and maintained as separate values for montages during a program run. Set to 1 to have the metadata option on by default for montages; 2 to have the file type be numbered TIFFs for montages, 3 for both of these settings to be on, or 4 for neither to be on.  The default is 1, to give .mdoc files for montages.
BackgroundSaveToFile Set to 1 to enable saving to file in a background thread, or 0 to disable it.  This was turned on by default in version 3.4.0 beta, so 0 is needed to disable it.

Microscope properties

DeltaZtoDefocusFactor Factor needed to adjust for a discrepancy between the change in defocus reported by the microscope and the actual defocus change. Determined by calibrating autofocus, moving in Z and measuring defocus; the factor is (defocus change)/(change in Z height)
StandardLowMagFocus A standard focus value for doing montages and calibrations in LM mode. On an FEI scope, a value of 0, representing 'eucentric focus', should be adequate, unless a different focus minimizes image movement when the beam is moved. With a value of -999, no standard focus is asserted when montaging or calibrating. The value for a particular focus setting can be determined with the ReportFocus script command. The default is 0 for an FEI scope and -999 for a JEOL or Hitachi. This entry is overridden by any calibrations made with Standard LM Focus in the Calibrate menu.
ScreenCurrentFactor Factor needed to give a calibrated current in the screen meter
SmallScreenFactor Additional factor needed to get the same current reading when switching between main screen and small current, with the beam filling the main screen
LensNormalizationDelay Time delay after projector lens normalization, in milliseconds, to be added to a built-in 800 msec delay before exposure starts.  The default is 2000.
LowMagNormalizationDelay Time delay after projector lens normalization in Low Mag mode, in milliseconds.  The default is to use the 'LensNormalizationDelay'.  Some Krios's need a value around 10000.
PostProbeDelay Time delay in msec after changing TEM probe mode on an FEI scope before an exposure starts; default 3000.
LowestMModeMagIndex Index of the lowest magnification in M mode, needed to prevent the task routines or filter control from switching into LM mode, and to indicate that image shift calibrations are not congruent across the LM-M boundary
HighestLMindexToScan If magnifications in LM are disabled above a certain point, add this property with the index of the highest enabled LM mag (i.e., the number of enabled LM mags) before running List Mags.
LowestGIFModeMagIndex Index of lowest magnification that should be used for tasks with the GIF camera. The default is to use the LowestMModeMagIndex.
LowestSecondaryModeMag Index of lowest magnification in a secondary mag range.  On the JEOL, this is assumed to be SAMAG.  The default is 0 for no secondary mag range; with a non-zero value, List Mags will list MAG mode then SAMAG mode and indicate the correct value.  On a Hitachi, this property must be entered with the index of the first magnification in HR mode.
NumberOfSpotSizes Number of spot sizes on the microscope; default is 11.
IntensityToC2Factor This entry is no longer needed; instead, the factor is measured by a calibration procedure and stored in the Calibrations file
UseIlluminatedAreaForC2 This entry must be set to 1 on a Titan Krios in order to calibrate and manipulate intensities.  It makes the program access illuminated area information instead of the ordinary C2 intensity setting.
IlluminatedAreaLimits Lower and upper limits of the illuminated area readout in microns divided by 100.  When set, this range of illuminated area will be mapped internally to intensities of 0.1 to 0.9, thus preventing the program from seeing out-of-range intensity values.  There is no default mapping.  If this property is added, it will invalidate existing beam and spot intensity calibrations and the crossover calibration.
C2ApertureSizes For a Titan, follow this with the list of available C2 apertures, without decimal points.
UseInvertedMagRange Set to 1 to stay in the range of high magnifications where the order is inverted when doing various procedures that require a minimum field of view.  By default, the program will ignore these mags when searching for the mag with a minimum field of view and go into the normal low end of nonLM mags.  Script commands that step through mags will reverse direction in the inverted mag range, as will many mag spinners in dialogs.  From the highest regular mag, an increase will step down into the highest inverted mag.  From there, an increase steps back up to the highest mag and a decrease steps down as desired.
TiltAxisOffset Distance from the optical axis to the tilt axis, as indicated by the Refine Eucentricity routine. To determine this value, run the routine 3-5 times near (within 100 microns) of the center of the grid.
StageLimits Limiting coordinates for stage movement in microns: minimum and maximum X coordinate, and minimum and maximum Y coordinate. The default is +990 or -990 microns for both FEI and JEOL scopes; a 0 may be entered to use the default.  For access to the full range of motion on a JEOL, enter '-1190 1190 -1190 1190'.  This is not the default for JEOL because the +/-990 limits were present for many years before anyone complained.
MaximumTiltAngle Set to the maximum angle that can be tilted to without generating an error.  The default is 79.9; Titan needs 69.9.
StageMoveDelay Delay time in milliseconds from moving the stage to taking any kind of picture, to be added to a built-in 800 msec delay before exposure starts. Default is 2000.
MinimumTiltDelay Minimum delay time in milliseconds from tilting to taking a picture where the user's tilt delay is not ordinarily imposed, to be added to a built-in 800 msec delay before exposure starts. The default is 200.
InvertStageXAxis Set to 1 to indicate that the stage coordinate system is left-handed when projected onto the screen. The axes of this coordinate system are assessed by noting the direction that the image moves when stage coordinate is increased in X or Y; if the direction for X is 90 degrees counterclockwise from the direction for Y then this property is needed (and a global rotation of 180 degrees may also be needed.)
RotateHeaderAngleBy180 If the tilt axis rotation angle defined by these properties results in reconstructions with inverted handedness, set this entry to 1 to rotate the angle output to the image file header by 180 degrees and restore the handedness. This will probably be needed if InvertStageXAxis is set.
FloatingCurrentMeterSmoothed 0 for no smoothing or 1 for smoothing of current readings when the floating current meter is opened
CurrentMeterLogBase Base value added to screen current in nanoamps, before taking the log for smoothing. Adjust this to make the smoothing behave similarly for large and small currents (default 0.02).
CurrentMeterSmootherThreshold1 Threshold change for a single value to trigger a change in the displayed, smoothed value (in log units, default 0.007).
CurrentMeterSmootherThreshold2 Threshold change in the running mean that will trigger a change in the displayed value (in log units). Change these two thresholds together to adjust smoothing.  Default is 0.0035.
WatchGauge Add a gauge to be watched for the VAC indicator in the microscope status panel. Follow this entry with the official name of the gauge (e.g., column vacuum IGP1 is P4 through Tecnai 3.0, but for Titan or Tecnai 4.0, it must be the name of the gauge in the user interface, IGP1 for Tecnai, IGPCl for Titan, IGPco for Talos), the threshold between a green and yellow reading, and the threshold between a yellow and red reading, in Pascals. A formula based on several simultaneous observations of Pascals and FEI log units for IGP is:

Log reading = 26.2 * log(Pascal reading) + 135

Or, Pascals = 10 ** ((log reading - 135) /26.2)

ShowIntensityCalStatus Set to 0 to disable the color-coded background on the word 'Spot' in the microscope status panel, which indicates whether intensity is in a calibrated range.
MicronsPerUnitImageShift A parameter that is used in the initial calibration of image shift (or when calibrating 'from scratch'). The right value is needed to get shifts that are big enough, but not too big, in the first round of calibration. For an FEI scope, this may need to be set to something besides 1 ff image shift is not properly calibrated in the scope alignments. For JEOL, a value of 0.02 is needed at 200 KV; a value of 0.1 is needed at 300 KV.  For Hitachi, a value other than 1 may be needed for calibrating HR mode.
LowMagMicronsPerUnitIS Scaling factor needed for initial calibration of image shift in low mag mode. If this is omitted, the factor specified in MicronsPerUnitImageShift is used. For JEOL, a value of 1 is needed at 200 KV, 1.5 at 300 KV.  For Hitachi, a value of 8 is needed.
ImageShiftLimit Limit on image shift at regular magnifications; image shifts are tested against this limit in some but not all situations. The default is 15 microns.
LowMagShiftLimit Limit on image shift in LM mode; image shifts are tested against this limit in some but not all situations. The default is 150 microns.
MaxCalibrationImageShift Maximum image shift change when calibrating image shift
MaxLMCalibrationImageShift Maximum image shift change when calibrating image shift at LM-mode mags.
ISoffsetCalStageLimit Maximum stage shift allowed during calibration of image shift offsets between magnifications. The default is 0.025 micron.
StageCalibrationBacklash Microns of movement to adjust for backlash in the stage calibration procedure. The default is 5 microns for FEI scopes, 10 microns for JEOL, and 20 microns for Hitachi.  This entry must be positive; a negative entry makes it use the default.
StageCycleLengthX Cycle length at which modulations in position error repeat for stage movements in X, which is used to control the extent of stage calibrations in X. Calibrations will traverse a multiple of this distance in X unless limited by the MaxStageCalExtent or by the possible number of steps. The default is 61 microns on FEI scopes (found on two Tecnais), otherwise 40 microns.
StageCycleLengthY Cycle length of modulations in stage position error in Y, used to control the extent of stage calibrations in Y. The default is 42 microns on FEI scopes, otherwise 40 microns.
MaxStageCalExtent Maximum distance over which to do the stage calibration. If this is larger than the cycle lengths in X and Y, it will allow calibrations to go over one cycle length, but may limit the number of cycles traversed at very low mag. A value lower than a cycle length will keep the calibration from being done over a full cycle on that axis. The default is 140 microns, which limits the extent to 2 cycles in X and 3 cycles in Y with the default cycle lengths.
SamePositionTolerance Maximum stage shift at which the program will still consider the stage to be at the same position as after it has moved the stage (used for keeping track of backlash).  The default is 0.1 microns for FEI and 0.2 micron for JEOL.
UseTrialSizeForShiftCal Set to 1 to use the image size in the Trial control set for image and stage shift calibrations.
UseTrialBinningForShiftCal Set to 1 to use the binning in the Trial control set for image and stage shift calibrations.
MagnificationTable A table of magnification index, film and screen magnifications, and the rotation angles reported on an FEI scope. The line with this entry must contain the number of table entries to follow, then there must be that many lines following. The form of each line is: 
    Index   Film mag    Rotation angle    Screen mag
The first three entries can be obtained by selecting List Mags in the Calibration menu. The screen mag must be added by hand. On a JEOL or Hitachi, the third entry can be omitted unless there is a GIF, in which case a 0 should be entered. If there is a GIF, each line should have three more entries:
    Mag with screen up    Rotation angle    Mag with screen down
Again, the third entry can be omitted on a JEOL.  For Hitachi, this table must be constructed by hand, listing each mag in low mag, then HC mode, then HR mode, and numbering them sequentially from 1.
CameraLengthTable A table of camera lengths, needed on the JEOL to recognize diffraction mode and on Hitachi to manipulate camera length in diffraction mode. The line with this entry must contain the number of table entries to follow, then there must be that many lines following. The form of each line is:
    Index    Camera length in mm
This table is obtained on a JEOL by selecting List Mags in the Calibration menu and appears after the magnification table. On Hitachi, it must be constructed by hand, listing each length found in HC mode
ImageShiftDelays A table of delays to apply after an image shift. The delays are applied before taking an image, and they are scaled up or down in some situations. They are also adjusted up or down for camera startup and clearing times lower or higher than 0.8 seconds. The line with this entry must contain the number of entries to follow, then there must be that many lines of the following form:
    Distance in microns     Delay in seconds
ISdelayScaleFactor Overall factor for scaling the delay to apply after an image shift.  The default is 1.0.  Use  Set IS Delay Factor in the Calibrate menu to assess the needed factor; see the instructions there.
ExtraISdelayPerMagDoubling This entry controls an increase in the image shift delay at magnifications where the pixel size of a Record image is smaller than 1 nm. With the default value of 0.25 second, 0.7 * 0.25 is added to the delay with a pixel size of 0.75 nm, 0.25 is added for 0.5 nm, 1.4 * 0.25 for 0.375 nm, 0.5 is added for 0.25 nm, etc.
LowDoseBeamNormDelay In low dose mode, the condenser lenses can be normalized by passing through the intensity and spot size of the View area when changing areas (needed on some JEOL scopes). This value sets the delay in milliseconds after going to the View parameters (default 100 ms).
LowDoseBeamTiltShifts Set to 1 to apply beam tilt changes when going between low dose areas; with this enabled, beam tilt changes will be recorded when the user sets up beam shift changes, just as for beam shifts.
MagChangeIntensityDelay Delay time between changing magnification and changing intensity.  The default is 200 msec on JEOL, 30 msec on Hitachi, and 0 on FEI.
FocusChangeDelay Delay time in milliseconds after changing focus.  Default is 0.
UpdateBeamBlanker Set to 1 to have the scope update routine monitor the state of the beam blanker instead of assuming that it is what SerialEM set it to, or 0 not to.  The default is 1 only if there is an FEI camera.  This is not implemented on JEOL.
BlankDuringTransients Set to 1 to blank the beam during spot size and magnification changes and lens normalizations.  Transients during these operations may get through the normal camera blanking and cause a K2 to retract.
CheckPosOnScreenError For an FEI scope only, set to 1 to have the program wait and see if the screen ends up in the desired position after an error occurs moving the screen.  It will wait up to 15 seconds.
PiezoScaling # # # # # Scaling and range information for a piezo drive controlled by a piezo plugin.  Follow with 6 numbers: plugin number (numbered from 0); number (from 0) of the piezo driven by that plugin; 1 if this is the Z or only axis, or 0 if it a scaling for X/Y axes; minimum and maximum raw position values for that piezo; and the scaling from microns to raw units.  Whenever a scaling is defined, the script commands for setting and reporting that piezo will use positions in microns.  A negative scaling can be entered, in which case scaled positions will be negative.
UsePiezoForLDAxis # # Use the Z or only position of a piezo to move  the stage instead of using image shift to go between low dose areas.  Follow with 2 numbers: plugin number (numbered from 0); number (from 0) of the piezo driven by that plugin. The 'PiezoScaling' property must also be entered to use this feature; it may be necessary to enter a negative scaling there to make the direction of movement match that given by image shift.
PiezoFullDelay # [#] [#] Delay time and optional factors after an on-axis movement in Low Dose; follow with the delay time for a full-range movement, in seconds (default 20); an optional factor by which to reduce the delay for Focus (default 0.6); and an optional factor by which to reduce the delay for Trial and View (default 0.3).

Autofocus, Autotuning, and Autoalignment properties

AlignTrimFraction Fraction to trim off edges of images for autoalignment correlations (default 0.04).
AlignTaperFraction Fraction of image to taper to mean over for autoalignment correlations (default 0.1).
AlignFilterSigma1 Sigma of inverted Gaussian that filters out low frequencies in autoalignment correlations (default 0.03)
AlignFilterSigma2 Sigma of Gaussian rolloff for filtering out high frequencies in autoalignment correlations (default 0.05)
AlignFilterRadius2 Radius at which high-frequency Gaussian rolloff starts (default 0.25).
FocusPadFraction Fraction to pad images for autofocus correlations (default 0.1).
FocusTaperFraction Fraction of image over which to taper to mean for autofocus correlations (default 0.1).
FocusFilterSigma1 Sigma of inverted Gaussian that filters out low frequencies in autofocus correlations (default 0.04).
FocusFilterSigma2 Sigma of Gaussian rolloff for filtering out high frequencies in autofocus correlations (default 0.05).
FocusFilterRadius2 Radius at which high-frequency Gaussian rolloff starts (default 0.25)
FocusMaxPeakDistanceRatio If the highest peak in the autofocus correlation is at 0,0, the program may reject this peak and use the second highest one, if the distance from target defocus implied by the second peak position is less than this ratio times the distance implied by the peak at 0,0. Smaller values make the peak rejection more conservative, 0 disables it. The default is 3.
FocusPostTiltDelay Delay time in msec between tilting the beam and starting to acquire the next image in a focus-detection sequence; the default is 0.
FocusViewNormDelay Delay time in msec between changing to View area in Low Dose and starting autofocus when the option to normalize through View is selected.  The default is 500.
AstigmatismParams B [A] [T] [F] [R] Default beam tilt for astigmatism calibration and/or correction (default 3.2).  A setting made through Focus - Set Astig Beam Tilt will be retained in the settings file and override this default.  Additional entries are optional: 'A' for stigmator values to apply (default 0.1); 'T' for threshold stigmator change above which the correction is iterated (default 0.015); 'F' for middle focus value at which stigmators are varied (default -1 microns); 'R' for focus range to assess (default 10 microns).
ComaParams B [F] Default maximum beam tilt for coma-free calibration (default 10).  A setting made through Focus - Set Coma Beam Tilt will be retained in the settings file and override this default. The optional 'F' entry is the focus at which coma-free operations are done (default -1).
AstigmatismComaDelays A [F] [B] Settling time after changing astigmatism in msec; this delay is done through settling before taking an image, which always adds 800 msec, so the default of 900 msec  gives a delay of 1700 msec.  The optional 'F' is the delay after changing focus in the astigmatism or coma-free routines (default  500 msec).  The optional 'B' is the delay after changing beam tilt for the coma-free routines (default 500 msec); it is applied only if it is larger than the delay set with FocusPostTiltDelay.

Task and montage operation properties

LimitMontageToUsable Set to 1 to limit montage frame size to the usable area of the camera and avoid gray borders in montage pieces.
MontageInitialPieces Number of pieces in X and Y to show initially in the montage setup dialog. The default is 1, 1.
MontageOverlapFraction Fraction of overlap to use when computing initial overlaps shown in the montage setup dialog when using image shift. The default is 0.1.
MontageDriftRepeatLimit Maximum number of times to repeat autofocus until drift is below the selected rate.  The default is 5.
MontageDriftRepeatDelay Delay time in seconds before repeating autofocus.  The default is 2.
MontageDuplicateRetries Maximum number of retries when a duplicate image is received from an Eagle camera when montaging. Set to -1 to disable testing for duplicates. The default is 3.
MontageaAutosaveLog Set to 1 to save the log window after every piece is saved.  A new file will be created with a name based on the name of the montage image file, unless there is already a file open with such a name.
StageMontageBacklash Microns of movement to adjust for backlash when taking a montage with stage movement, and in some othe situations. Default is 5 microns for FEI, 10 microns for JEOL, and 20 microns for Hitachi.  This entry must be positive; a negative entry makes it use the default.
StageRelatxation Microns of movement to apply opposite to the last stage movement, available in specific situations to reduce drift.  Default is 0.025.
StageMontageMaxError Maximum error in stage position allowed when doing a stage montage, in microns, followed by a 1 to stop after trying to reach the stage position 3 times, or a 0 to go on. The default, 0, means that the position will not be tested after a move. Errors up to 0.26 are normally seen with a JEOL.
MontageRealignToNearest Set to 1 to have the periodic realignment to a nearby piece using stage shift align to the nearest piece instead of to a piece near the middle of the column.
MontageFilterR1R2S1S2 Primary filter settings for montage correlations, in cycles/pixel with the standard IMOD definitions: radius1 for correlations with very sloppy montages (the negative of the frequency at which the low frequency filter starts rising from 0, so it should be negative or 0), radius2 (start of high frequency rolloff); sigma1 (sigma for rise of low frequency filter); sigma2 (sigma for falloff of high-frequeny filter).  All four values must be entered.  The default is -0.01 0.35 0.05 0.05.
MontFilterSet2R1R2S1S2 Second set of filter settings for montage correlations, in the same format as for 'MontageFilterR1R2S1S2'.  All four values must be entered.  The default is 0 0.35 0.05 0.05.
CheckAutofocusChange The change in defocus that will be applied in the positive and negative direction when the routine to check autofocus is run (default 5).
ResetRealignMaxIterations Maximum number of iterations when the routine to reset image shift and realign is run (default 2).
ResetRealignIterationCriterion If image shift exceeds this criterion after resetting the image shift and realigning, another iteration will be done, up to the maximum number of iterations (default 0.5).
ResetRealignHigherMagCriterion If image shift is less than this criterion when doing the reset and realign task, then the alignment pictures will be taken at one mag step higher than the default (default 1.7).
WalkUpMaxInterval Maximum tilt interval for the walk up task (default 8).
WalkUpMinInterval Minimum tilt interval for the walk up task. Intervals will initially be the maximum interval times the cosine of the tilt angle, but will not become smaller than this minimum (default 3).
WalkUpShiftLimit When image shift exceeds this limit during the walk up task, the reset and realign operation will be run.
WalkUpLowDoseISLimit A similar limit on image shift, applied when walking up in low dose mode.
EucentricityBacklashZ Amount to move in Z to correct for backlash when changing Z during the eucentricity routines (default -3).
EucentricityCoarseInitialAngle Starting tilt angle for the coarse eucentricity task (default -5).
EucentricityCoarseInitialIncrement Starting tilt increment for the coarse eucentricity task (default 0.6).
EucentricityResetISThreshold Image shift will be reset to zero, and the stage moved to compensate, if it exceeds this criterion before a eucentricity task (default 0.1).
EucentricityCoarseMaxTilt Maximum tilt angle for the coarse eucentricity task (default 10).
EucentricityCoarseMaxIncrement Maximum tilt increment for the coarse eucentricity task (default 8).
EucentricityCoarseTargetShift The coarse eucentricity routine will increase the tilt increment to try to make the image shift by this amount in microns (default 2).
EucentricityCoarseMaxIncrementChange Maximum factor by which the tilt increment will change from one trial to the next in the coarse eucentricity task (default 3).
EucentricityFineIterationLimit Maximum number of iterations for the fine eucentricity task (default 3).
EucentricityMaxFineIS Maximum image shift for the fine eucentricity task before it changes Z height and starts a new iteration (default 2).
ResetRealignMinField Minimum camera field of view, in microns, for resetting image shift and realigning, which determines the mag used. Default is 7.
ReverseTiltMinField Minimum camera field of view, in microns, for the reverse tilt task. Default is 4.5.
EucentricityCoarseMinField Minimum camera field of view, in microns, for the coarse eucentricity task. Default is 9.
EucentricityFineMinField Minimum camera field of view, in microns, for the fine eucentricity task. Default is 4.5.
EucentricityFineAlignMinField Minimum camera field of view, in microns, for doing fine eucentricity and maintaining image alignment. Default is 9.
WalkUpMinField Minimum camera field of view, in microns, for the walk up task. Default is 1.5.
TiltAfterMoveMinField Minimum camera field of view, in microns, for realigning after a tilt following a stage move. If the value is non-zero, this task is invoked during walk up and tilt series on the tilt after an image shift reset. The default is 0. for FEI scopes and 4.5 um for JEOL.
BacklashAdjustMinField Minimum camera field of view, in microns, for the X/Y backlash adjustment routine run by the Navigator. Default is 6.0.
TiltBacklash Amount to tilt to eliminate tilt backlash.
MinTaskExposure Minimum exposure time allowed, when it is necessary to reduce the exposure time upon going to a lower magnification (i.e., when intensity cannot be reduced enough). This minimum will apply both for tasks and for low magnification tracking in a tilt series. The default is 0.002, but a higher value may be needed if camera shuttering is slow and exposures of this duration give no image
RefineZLPStepSize The step size in eV for the Refine ZLP procedure. Default is 2.
RefineZLPSlitWidth The slit width used for the Refine ZLP procedure. Default is 20 eV.
RefineZLPMinimumExposure The minimum exposure used in the refine ZLP procedure, in seconds. The procedure uses the Trial parameter set in normal mode and the Preview parameter set in Low Dose mode, with the exposure reduced by a factor of 10, but not below this minimum. The default is 0.005, but numbers as low as 0.002 can be used if the number of counts is consistent within a few percent from one exposure to the next.  However, a higher value will be needed if camera shuttering is slow; values of 0.02 to 0.05 are often needed on JEOLs.
RefineZLPMaxMeanRatio The maximum ratio between the final and peak mean counts in the refine ZLP procedure, i.e. the counts after the slit is moved to the left of the ZLP must fall below the peak counts when the slit is over the ZLP by this ratio or less. Raise this ratio if the ZLP fails to be recognized. The default is 0.02.
RefineZLPRedoInLowDose Set to 1 to have the Refine ZLP procedure retry 10 eV below and 10 eV above the original energy upon failure in low dose mode, just as it does in regular mode. The default is to quit upon failure in low dose mode.
EnergyShiftCalMinField Minimum camera field size for the lowest mag that will be done when calibrating mag-dependent energy shifts. This should be set to the largest minimum field size for any of the tasks. The default is 8 microns.
CookerRealignMinField Minimum camera field of view, in microns, for images used to realign after cooking a specimen. Default is 8.
CookerISLimit Limit on image shift for the specimen cooker: after it takes an image and realigns to it, it will reset image shift if it is above this limit and take a new image for realigning. Default is 2.
CookerScreenTiltDelay This property is no longer needed in SerialEM 3.6.
DistortionStageDelay Delay time between moving stage and taking an image for distortion pairs, in milliseconds.  The default is 0, which means to use the time set by 'StageMoveDelay', whose default is 2000.
StageTimeoutFactor Factor by which to multiply allowed time for stage movements to complete; default is 1.  Originally applied only to stage movements in eucentricity tasks, additional applications will be added as needed.

Tilt series controller properties

TSDefaultStartAngle

Default angle for starting and ending tilt series, when controller
is not invoked at high tilt

TSMaxUsableAngleDiff Maximum tilt angle difference between images that can be cross-correlated; this value is reduced by the cosine of the tilt angle in deciding whether an image is usable as a reference for alignment (default 10).
TSBadShotCrit The fraction of expected counts that an image must contain to be accepted and not considered a bad shot (default 0.2).
TSBadLowMagCrit The corresponding fraction for images obtained at a lower magnification, where intensities may not be set as accurately (default 0.1).
TSMaxTiltError Maximum error allowed in setting tilt angle before the TSC decides that a pole touch has occurred.  The default is 0.1; it needs to be set to at least 0.2 on a JEOL.  This value also sets a minimum threshold for detecting whether tilting has reversed direction, for which the default is 0.1 on FEI and 0.2 on JEOL.
TSMaxDelayAfterTilt Maximum delay time after tilting allowed to be entered in the tilt series setup dialog, in seconds.  The default is 15.
TSBidirAnchorMinField The first number entered sets an advisable minimum field size for the starting anchor image of a bidirectional series; below this level, the field size will be shown in bold with two stars in the setup dialog.  The default is 8 microns.  An optional second number sets a size below which the field size is shown with four stars; the default is 6 microns.
TSLowMagFieldFrac When low mag tracking is enabled, it will be used if the error in the last prediction was bigger than this fraction of the field (default 0.3).
TSStageMovedTolerance When resuming from a stop, the user will be assumed to have moved the stage and disturbed predictability if any one of X, Y, or Z is bigger than this number (default 0.1).
TSUserFocusChangeTol When resuming from a stop, focus predictability is considered disturbed if the difference between microscope defocus and the autofocus target has changed by more than this amount (default 0.1).
TSFitDropErrorRatio When doing a fit, if the ratio of the standard error with all points included to the best error with the maximum number of points excluded is bigger than this value, points will be dropped (default 1.3).
TSFitDropBackoffRatio Once the decision is made to drop points, points will be dropped until the standard error falls below the minimum standard error times this ratio (default 1.1).
TSMaxImageFailures The maximum number of retries after a image is acquired that does not have enough counts (default 3).
TSMaxPositionFailures The maximum number of retries after a Record image is acquired that loses more than the desired fraction of necessary image area (default 3).
TSMaxDisturbValidChange Maximum number of disturbances to look past for valid changes to include in the fits. A bad idea - default is 0.
TSMaxDropAsShiftDisturbed Maximum number of points to drop routinely from the fits for X or Y after a disturbance in position (default 3).
TSMaxDropAsFocusDisturbed Maximum number of points to drop routinely from the fits for Z after a disturbance in focus (default 2).
TSXFitInterval Maximum angular interval over which to fit X coordinates (default 8).
TSYFitInterval Maximum angular interval over which to fit Y coordinates (default 12).
TSZFitInterval Maximum angular interval over which to fit Z coordinates (default 12).
TSXMinForQuadratic Minimum number of points to fit X coordinates to a quadratic curve rather than a line (default 4).
TSYMinForQuadratic Minimum number of points to fit Y coordinates to a quadratic curve rather than a line (default 4).
TSMinFitXAfterDrop Minimum number of points to retain in fit for X when dropping points (default 5).
TSMinFitYAfterDrop Minimum number of points to retain in fit for Y when dropping points (default 5). 
TSMinFitZAfterDrop Minimum number of points to retain in fit for Z when dropping points (default 4).
TSTrialCenterMaxRadFrac When centering beam from Trial image, maximum fitted radius of the beam that is acceptable for moving beam as a fraction of the image diagonal (default 0.45).
TSEarlyK2RecordReturn Set to 1 to have Record or Extra Record images on a K2 camera with saving of dose-fractionation frames return as soon as the full summed image is ready, with frame saving done asynchronously.  This can allow tracking shots to be done earlier, the time difference is especially significant when saving super-resolution frames and/or compressed TIFF files.  Works only with GMS 2.3.1 or higher.

Navigator properties

ConvertMapsToBytesDefault Set to 0 to have the option to convert maps to bytes be off by default.
RealignItemMinMarginNeeded When running Realign to Item, Navigator must find a map containing
the item with at least this much distance from the center of an image
frame to the edge of the map. The default is 1.5 microns.
RealignItemMaxMarginNeeded When running Realign to Item, maps with a greater distance from the center of an image frame to the edge of the map will be preferred for the first round of aligning to a frame of the map; but all distances greater than the value here will be treated equally. The default is 10 microns.
RealignItemMinMarginWanted When running Realign to Item, a frame that is closer to the target will be preferred for the first round of alignment as long as the distance from the frame center to map edge is bigger than this value. The default is 5 microns.
RealignItemMaxIS Maximum movement to target position in first round of realigning to an item that can be done with image shift instead of stage shift.  Default is 1 micron.
RealignItemMaxLMField Maximum camera field of view to allow when considering whether to realign to an LM map.  This can be set to about half the size of the smallest objective aperture that might be present during the realign operation.  The default is 15 microns, suitable with a 30-micron aperture.
RealignItemWeightCCCThresh Threshold distance for weighting the cross-correlation coefficient when correlating with multiple montage frames in Realign to Item.  When the intial stage move error implied by the correlation position is greater than this threshold, the CCC is divided by the error distance. 
RealignItemWeightingSigma Sigma value for a Gaussian weighting by distance from zero shift for the correlation coefficient in the second round of Realign to Item, where the overlap between correlated images at zero shift is often less than 100%, and the shift is expected to be low.  The default is 3 microns; a smaller value could be tried if correlations find the wrong hole in a regular hole pattern.
RealignItemSkipCenTime The first round of alignment in Realign to Item is to the center of a map frame.  This alignment will be skipped if the time in minutes is less than the amount entered here since the last alignment to that frame center.  The default is 15 minutes; an entry of -1 would disable this feature.
RealignItemSkipCenError In the second round of alignment, to the target position, the program will evaluate the error and disallow skipping the first round if it is greater than 1/6 of the image size.  In addition, if a maximum error in microns is entered here, the program will disallow skipping when the error exceeds this amount AND it will extend the lifetime of the skipping capability when the error does not.  This extension does not happen if this property is not entered.
RealignItemUseBeamOffsets Set to 1 to apply the relative offsets between Record and View mode for beam shift (and beam tilt, if that is being recorded) when realigning to a map taken in Low Dose View mode.  This adjustment is useful for JEOL scopes where View mode has a different alpha and has not been tested in other situations.
RealignItemTiltTolerance Realign to Itrem will tilt to the angle at which the map was taken if it differs from the current tilt angle  by more than this amount times the cosine of the tilt angle (or times 0.5 above 60 degrees).  The default is 2 degrees.
RealignItemFocusChangeLimit If non-zero, then Realign to Item will leave Low Dose mode for realigning to a View or Search mode map if the map's defocus offset differs from the current offset by more than the given amount.  Should be useful only for testing behavior when leaving low dose.
ImportStageToImage Stage to image transformation for images imported as maps. Enter 4 numbers and an optional name; the values are the number of pixels in X per micron in X, pixels in X per micron in Y, pixels in Y per micron in X, and pixels in Y per micron in Y. Y coordinates are inverted; i.e. Y is 0 at the top of the image. If no name is entered, one will be synthesized from these values. Multiple transformations can be entered.
ImportTiffIDField Use this entry to define a TIFF tag whose value can be used to uniquely identify which import transformation applies to an image. Follow with 5 values: 1) the number of the import transformation, where the first transformation entered with 'ImportStageToImage' is numbered 1 and 0 refers to the 'None' transformation; 2) the TIFF tag (e.g., 282 for X resolution); 3) the type of tag: 1 or S for unsigned 16-bit integer, 2 or I for unsigned 32-bit integer, 3 or F for float, 4 or D for double, 5 or C for character; 4) The element number, numbered from 1, if the tag contains an array, or 0 for a simple value tag; 5) the expected value of the tag.
ImportTiffXField Use this entry to define a TIFF tag from which the X stage coordinate of the image can be extracted. Follow with items 1) to 4) described for 'ImportTiffIDField'
ImportTiffYField Use this entry to define a TIFF tag from which the Y stage coordinate of the image can be extracted. Follow with items 1) to 4) described for 'ImportTiffIDField'
ImportSubtractFromTIFFStage Values to subtract from the X and Y stage coordinates extracted from a TIFF file.
GridInPolygonBoxFraction When a grid of points is added to fill a polygon, the program includes a point in the grid only if a square around the point is fully contained in the polygon. The size of this square is a fraction of the spacing between points. This entry can be used to change the fraction, whose default value is 0.75.
NavigatorStageBacklash Amount of backlash to apply in Navigator stage movements, in microns, to points where a backlash direction has not been otherwise defined, such as by being marked on a montage map.   This setting would allow such points always to be approached from the same direction. The default is 0.
NavigatorMaxMontageIS The maximum amount of image shift allowed, in microns, when fitting a montage to a polygon in non-low mag; the montage will be constrained to stage movement if image shift exceeds this amount. The default is 7, which is generally too large for a Tecnai F30 and JEOLs with limited image shift, and may be too restrictive for other scopes. If needed image shift is above this limit when not fitting to a polygon, the Montage setup dialog asks the user if they want to change to stage movement.
NavigatorMaxLMMontageIS The maximum amount of image shift allowed, in microns, when fitting a montage to a polygon in low mag mode; the default is 35. If needed image shift is above this limit when not fitting to a polygon, the Montage setup dialog asks the user if they want to change to stage movement.
FitMontageWithFullFrames Set to a number between 1 and 2 to use the full frame size in montages fit to polygons.  With 1, the overlap is unchanged and the captured area will be bigger; with 2, the overlap is increased as much as possible to keep the captured area the same.  For a number between 1 and 2, the value minus 1 is the fraction of the extra area per frame used to increase overlap instead of captured area.

Beam intensity calibration properties

Note that these properties changed completely with the change to CCD-based calibration in SerialEM 2.4.1

BeamCalMinExposure Minimum exposure time for calibration images (default 0.1 sec)
BeamCalMaxExposure Maximum exposure time for calibration images (default 3 sec)
BeamCalMinCounts The minimum number of counts in a calibration image (unless exposure time is at the maximum), before division by 2 for 16-bit camera, if any. The default is 100.
BeamCalMaxCounts The maximum number of counts in a calibration image, before division by 2 for a 16-bit camera, if any. This should be set to about 2/3 of your camera's saturation level. The default is 8000.
BeamCalSpacingFactor Spacing between brightnesses measured, as a multiplicative factor (default 1.1)
BeamCalChangeDelay Delay in milliseconds after setting a new beam intensity (default 400).
BeamCalInitialIncrement Initial change in C2 intensity value (default 0.0002).
BeamCalMinField The minimum camera field of view at which beam calibration will be needed; should correspond to the biggest minimum field size required for any of the tasks (default 8 microns)
BeamCalExtraRangeNeeded Additional range in intensity to be calibrated beyond that needed to get the same intensity upon changing from the current mag to the lowest mag needed (default 10.)
BeamCalFavorMagChanges Set to 1 to change magnification in favor of increasing exposure or spreading the beam much, as is done with the K2 camera.
BeamCalUseTrialSettling Set to 1 to use the drift settling time and the shuttering type specified in the Trial parameter set; otherwise settling will be 0 and beam shuttering will be used.

JEOL properties

JeolUpdateByEvent Set to 0 to disable updating by events if this screws up.
UpdateSpectroscopyByEvent Set to 1 if the JEOL interface makes the promised event call when changing between spectroscopy and imaging modes.
InitializeJEOLDelay The delay between initializing the JEOL COM object and the first attempt to call functions, in milliseconds, if events are not being used for update. Without this delay, errors occur.
ScopeUpdateInterval The interval in milliseconds between calls to the function that reads scope properties and updates the user interface. The default is 100. For a JEOL, the update function does not normally access the microscope so this should be OK.
JeolUpdateSleep The sleep time, in milliseconds, between calls to the update function that actually queries the scope in a separate thread. If events are used for update, this function does one or two queries per call, taking up to 150 msec, so this interval must be long enough to leave substantial time for user interface handling, etc. If events are not used for update, the stage position and status calls take up to 300 msec.
JEOLReportsSmallScreen Set to 0 to indicate that the scope does not report the small screen position. Needed on 2100.
JEOLReportsLargeScreen Set to 0 or -1 to indicate that the scope does not report any detector at all representing the large screen position. If the large screen position is still reported by event but the call to read the screen position does not work, set to -1 to initialize the state as unknown; it should then be raised as needed for camera acquisition.  If there are no such events set it to 0 and the state will be initialized as up; the program should then not try to raise the screen.  Do not set this if an alternative main detector ID can be set.
JeolMainDetectorID Set this to indicate the ID of a detector whose position is reported and which needs to be retracted for camera imaging. The default ID is 13 for the main screen. Possible alternative IDs are 5 for upper TV camera and 17 for a lower TV camera.
JeolControlsBeamValve Set to 0 to indicate that the gun valve cannot be controlled (non-FEG).
HasOmegaFilter Set to 1 to indicate that the scope has an omega filter. The program will then enable the filter control panel but not do any of the mag changes, etc, involved in EFTEM mode.
UseJeolGIFmodeCalls Set to 1 to read GIF mode state directly from the microscope instead of deducing it from a string passed with magnification changes.  Set to 2 to allow the program to try to control GIF mode.  You can use the script commands "ReportJeolGIF" or "SetJeolGIF #" to assess whether the function calls for reading or changing the state work correctly. (Use a value of 0 or 1 to turn the mode off or on.)
PostJeolGIFdelay Delay time in msec after changing GIF mode on a JEOL; the default is 3000.
JeolHasNoAlpha Set to 1 to indicate that this microscope has no alpha setting. This seems not to be necessary but could be set if errors are generated from attempts to read or set alpha. This setting is implied when Jeol1230 is set.
Jeol1230 Set to 1 for a JEOL 1230; has many implications.
FocusTickTable Use this entry to start a table of the number of focus ticks for one click of the focus knob at various magnifications. Follow with the number of lines to follow. Then on each following line, put a mag index and the number of ticks. The default is 1 for any mag not entered here.
JeolForceMDSmode Set to -1 to turn off MDS mode and give a warning message upon program startup. 1 no longer forces the microscope into MDS mode on startup.
JeolPostMagChangeDelay Some versions of TEMCON generate errors when stage parameters are accessed too soon after a magnification change. In addition, when the program is updating scope status by receiving events, magnification changes generate many events that take significant time to be received. This entry can take one or two delay times in milliseconds. The first number specifies the delay for any scope accesses after the program changes mag. The second number provides for an additional time during which access to the stage will be deferred. If only one number is used, values of 2000 or more may be needed to prevent errors. With two numbers, values of 1000 and 3000 could be tried. The default is 1250 if updating by event, otherwise it is 0.
JeolMagEventWait Before changing the mag, the program will wait up to this amount of time since the previous mag change for its event to arrive. The default is 5000 msec, which should be quite generous.  When mag is changed too often, event delivery can fall behind and image shift can get off; but if a much longer wait is needed, then the VME should be restarted.
AlphaChangeDelay Delay time in msec after changing alpha on a JEOL as part of low dose area or other state changes.  The default is 500.
MagChangeFixISdelay If updating by event, the maximum possible interval from the time when a neutral image shift is reported to the time when the mag change responsible for the neutralization is reported. Default is 450 ms.
OtherShiftBoundaries List of mag indexes at which image or beam shift calibrations are not congruent with the next lower mag. Just like LowestMModeMagIndex, such an index indicates the start of a new mag range. Within a mag range, both the relation between image shift output and position on the specimen, and the relation between beam shift output and position on the specimen, should be constant.
JeolIndexForMagMode Set this to 3 to use the program with SAMAG instead of MAG mode; the default is 0 for MAG mode.  To use the program in both modes requires a separate set of property and calibration files for each mode, just as when setting up the program to work at multiple voltages.  See Setting up for Separate Voltage and follow the instructions about making a separate subfolder (e.g., SAMAG instead of 200KV) and making a second, modified shortcut to the program.
JEOLStageMotorRounding The value to which stage coordinates will be rounded before being used to drive the stage motors, in microns. Should be 0.001, which is the default. With the emulator 0.1 is needed; this will be set if SimulationMode is set to 1.
JEOLStagePiezoRounding If this value is non-zero, then after stage coordinates are rounded as indicated by JEOLStageMotorRounding, the remainder will be rounded by this value (in microns) and used to drive the piezoelectric positioners. With a value of zero, no piezo positioning will be done. Keep this at 0.
JEOLObjectiveLensToMicrons Scale factor for converting the objective lens fine digital readout to microns of defocus. The default is 0.0058, the value for 300 KV; it may need to be changed to make the defocus values in SerialEM match the values on the microscope display. For 200 KV the value should be 0.002.
JEOLObjectiveMiniToMicrons Scale factor for converting objective minilens values to microns in low mag mode. The default is 0.01 (measured on a 2100).
JEOLBeamShiftToMicrons Scale factor for rough conversion of beam shift values to microns. The default is 0.025, the value for 300 KV, which also works at 200 KV. It needs to be changed to get big enough spot movements in the first round of calibrating beam shift.
JEOLLowMagBeamShiftToMicrons Scale factor needed for calibrating beam shift in low mag mode. If this is omitted, the factor specified in JEOLBeamShiftToMicrons is used. A value of 0.15 works at 200 KV.
MicronsPerUnitImageShift See entry above in Microscope properties
LowMagMicronsPerUnitIS See entry above in Microscope properties
JeolUseProjectorForIS Set to 1 to substitute projector shift for image shift. Neutral value, image shift, and beam shift calibrations would need to be redone and kept in a separate calibration file when operating in this mode, and different values of the microns per unit image shift values may be needed.
JeolMMperUnitProjector When using projector shifts, this factor is used in the initial calibration of image shift; it specifies the approximate number of millimeters of shift on the camera per initially scaled unit of projector shift. The default is 1.5, based on scale matrices on a 2100 in which one unit of projector shift produced ~100 15-micron pixels of shift.
MessageBoxWhenClipIS Set to 0 to avoid having a message box appear when image shift goes beyond range and gets clipped to its limiting values.
ShootFilmIfMontageDark Set to 1 to retry taking an image after talking a film picture when a montage frame falls below the minimum counts set by the user with Set Minimum Counts in the Camera menu. This action may unstick a stuck lower shutter.

Hitachi properties

HitachiIPaddress IP address of Hitachi microscope server; the default is 192.168.10.1 and simulator may need 127.0.01. 
HitachiPort Port number of Hitachi microscope server; the default is 12050 and simulator may need 12053.
HitachiBeamBlankAxis Coil and axis to use for beam blanking and shuttering: 0 or 1 for X or Y axes of the gun shift coil or 2 or 3 for X or Y axes of the gun tilt coil.  The default is 0.
HitachiBeamBlankDelta Amount to change coil to blank the beam, a value between -1 and 1.  The default is 0.5.
HitachiPAforHRmodeIS Set to 1 to use projector shift instead of intermediate lens shift for image shift in HR mode.
HitachiTiltSpeed A value between 40 and 127 that controls tilting speed; the default is 100.  If it is 0, then the program will not set the tilt speed.
HitachiStageSpeed A value between 200 and 160000 that controls stage movement in X/Y nonlinearly.  The default is 80000, which is about equivalent to the speed of 9 in the Hitachi user interface.  If this value is 0, the program will not set stage speed.
HitachiImageShiftToMicrons Factor used by the plugin to scale image shift to approxiamte microns.  The default is 50.
HitachiBeamShiftToMicrons Factor used by the plugin to scale beam shift to approximate microns.  The default is 100.
HitachiObjectiveToMicrons Factor for scaling objective lens values to microns; the default is 10000.
HitachiI1ToMicrons Factor for scaling intermediate 1 lens values to microns in low-mag mode; the default is 10000.
HitachiScreenArea Factor for scaling current density value to current.
HitachiZMicronsPerGroove Number of microns of Z movement per groove on the Z knob.  The default is 3.1.
HitachiSpotStepDelay Delay time between changing spots when the program drops down to spot 1 and steps up to a desired spot number instead of decreasing the spot size. The default is 120.

STEM properties

STEMMagTable Start of magnification table for STEM.  The number of magnifications appears on this entry, and each following line has one magnification index and magnification value, as output by List Mags in the Calibration menu.
LowestSTEMnonLMmag Enter the index of the first STEM magnification not in Low Mag: one number for a JEOL, and two numbers for FEI, first for nanoprobe then for microprobe.
LowestMicroSTEMmag On an FEI, the index of the lowest microprobe magnification, as output by List Mags in the Calibration menu.
JeolSTEMmagUnitsAreX Set to 1 if calls to determine magnification on a JEOL return units 'X' instead of 'ABC'.  If the program fails to detect STEM mode, set DebugOutput to G and see if there are messages from LookupMagnification like 'JeolSTEM set but units X' and 'JeolSTEM state 1 does not match units X'.
JeolSTEMdefocusFactor Scaling factor needed to make changes in the defocus readout in SerialEM match changes in the JEOL interface.
STEMdefocusToDeltaZ Scaling factor to convert a defocus change to a difference in Z height, as output by STEM Focus Vs. Z in the Calibration menu.  There can be two numbers on this line, the first for nanoprobe mode and the second for microprobe mode.
STEMFocusVsZBacklash Size of backlash correction in the STEM Focus Vs. Z routine in the Calibration menu. The default is 3 microns for FEI and 10 microns for JEOL.
STEMCalFocusRange Default defocus range over which to run autofocus calibration.  The default is 8 microns; about 20 microns is needed on a JEOL 1400plus.
STEMMicronsPerUnitImageShift Rough scaling of image shift units to microns in STEM mode; by default it is set to value for MicronsPerUnitImageShift, but may need to be different (especially on JEOL) if there is not an appropriate initial image shift when calibrating image shift from scratch.
JeolUseCLA2ForSTEM Set to 1 to use CLA2 instead of CLA1 for STEM image shift on a JEOL.
STEMFocusShowBestAtEnd Set to 0 to keep the program from copying the best focused image to buffer A after autofocusing; this would be needed for 'Report on Existing' to work properly.
DynamicFocusInterval Interval in milliseconds for focus steps when using dynamic focus during an exposure.  The default is 40 msec for FEI and 80 msec for JEOL.
InitialDynamicFocusDelay Time in milliseconds to wait after setting the focus for the start of an exposure with dynamic focus.  The default is 100 for FEI and 250 for JEOL.
ImageDetectorIDs List of STEM detector IDs on a JEOL.  These IDs can be determined by setting the debug output key letter to 'e' and watching for events when detectors are inserted or retracted.  Detectors with IDs must be listed before ones without IDs in the Camera Properties section.
MutuallyExcludeDetectors Use this entry to indicate detectors that do not work together; follow with the numbers of the detectors (numbered from 0).  The program will not allow you to select them together.
MappedToDSchannel On a JEOL, use this entry to indicate a mapping between one or more detectors and the channels in DigiScan.  Follow with the number of the DigiScan channel then one or more detector numbers (all numbered from 0).
DetectorBlocks On a JEOL, use this entry to indicate that a detector with a JEOL ID blocks one or more other detectors when inserted.  Follow with the detector number of the one that blocks, and the numbers of one or more detectors that are blocked.
InsertJeolDetectorDelay Delay time between inserting a detector and acquiring an image on the JEOL (default 700 ms)
SelectJeolDetectorDelay Delay time between selecting a detector and acquiring an image on the JEOL (default 700 ms).
ShotTimeToInsertDetector Exposure time for the dummy image acquisition needed to insert detectors after entering STEM mode with FEI STEM.  The default is 3 sec.
DigiScanExtraShotDelay As of SerialEM 3.1.1, this entry has two effects: 1) it is the delay time between stopping continuous acquisition and deleting the parameters; 2) if it is non-zero, single-shot DigiScan images will be taken asynchronously with a loop to check if they are done, but if it is 0, images will be taken synchronously.  The latter will crash current versions of DM, but apparently not some future version.  The default is 100 ms.
DigiScanLineSyncWait Number of microseconds of waiting time to add when the Line Sync option is on for taking DigiScan images.  The pixel time will be constrained so that the pixel scanning time plus the flyback time plus this wait equals an integral number of line cycles.  The default is 10 microsec.
DigiScanFlipAndRotation Use this entry to be warned about harmful changes in the DigiScan Configuration dialog.  Follow with 2 numbers: 1 if Flip Horizontal Scan is checked or 0 if not, and the value that should be in the Rotation Offset field.
DigiScanControlBeam Follow with 1, 2, 4, or 8 to enable DigiScan to control beam position between shots and return it to a good position.  This requires GMS 2.2 or later.  With 1, it will move the beam to the safe position. With 2 or 4, it will move the beam to one-eighth of the field past the upper left or lower right corner of the image, respectively (as of November 2015, this requires a DigiScan patch to work).  With 8, it will simply retain control without any explicit beam positioning command.  Shots will be taken synchronously with a 17 ms delay at the end, regardless of the setting of DigiScanExtraShotDelay.
JeolSTEMrotation The rotation angle that should be set in the JEOL STEM user interface, a value from 0 to 359.  The program will set this angle when starting if this entry exists.
JeolSwitchSTEMsleep Follow with one or two values. If one value, it is the milliseconds to wait (with updates suspended) right after switching STEM mode on or off on a JEOL. If two values, they are the delays for switching into and out of STEM, respectively.
JeolSTEMPreMagDelay  Delay time in msec between the last image from a JEOL STEM camera and changing STEM magnification.  The JEOL STEM can lock up on a mag change if the delay is not long enough.  The default is 1500.
LowerScreenForSTEM Set this to 1 to have the screen lowered to override CCD camera blanking when trying to acquire an image in STEM, 2 to have the screen lowered immediately upon entering STEM mode, -1 to have the screen raised when acquiring an image in STEM, or -2 to have it raised immediately upon entering STEM mode.  The default is 1.
MustUnblankWithScreen Set this to 1 and LowerScreenForSTEM >= 0 if lowering the screen is the only way to override camera blanking.  This will disable the 'Retract to stop camera blanking' button in the STEM control panel.
RetractCameraOnEnteringSTEM Set this to 1 and LowerScreenForSTEM <= 0 to have cameras retracted with the beam blanked when STEM mode is entered.  This can be used to protect a pre-GIF CCD camera if the microscope unblanks the beam in STEM mode with the screen up (e.g., for accessing detectors under the screen).
InvertBrightField Use this entry to control when images from a channel whose name starts with 'Bright' have their contrast inverted.  With the default value of 1, these images will be inverted whenever the 'Invert contrast of image data' in the STEM Control panel is checked.  With a value of 0, they will never be inverted.  With a value of -1, they will be inverted when the button is NOT checked, so that bright and dark field images will always have the same contrast polarity.