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. The keywords are case-insensitive, but they are most readable when shown in the MixedCase form used here. 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 string that might have spaces, like a path entry or camera or detector name) cannot have a comment on the same line because it will be considered part of the entry.
The file can also have multiline comments starting with '/*' and ending on a line containing '*/'. The '/*' must be at the start of the line, whereas the '*/' can be anywhere on the ending line. This makes it easy to comment out a section of entries.
General entries
General camera control properties
Energy Filter 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
| 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 a Thermo/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. |
| AdvancedScriptingVersion | Set to 4 to indicate that the version of Advanced Scripting supports CFEG flashing and has autoloader and temperature control classes, as well as support for continuous recording from Ceta 2 cameras. The property is set to 4 automatically if there is a camera with 'FEIFilterType 1' set. Do not set this property unless you have a server version of at least 7.8 (Titan 3.8, Talos 2.8) or it will crash SerialEM or FEI-SEMserver when a function is called that does not exist in the current version. |
| UseUtapiScripting | Set to 1 to try to connect to the new Thermo/FEI UTAPI scripting, either on the local computer or at the address used to connect to FEI-SEMserver.exe. For testing, set to 2 to connect to UTAPI without trying to connect to the scope otherwise. |
| SimulationMode | Set to 1 or to a desired high voltage value to indicate a microscope/camera simulator is being used (enables some actions on JEOL and is needed to use an Eagle camera in simulation mode). Do not use this instead of NoScope with a real camera that uses dark references in SerialEM, since it also divides dark references by 8 and reduces the variation in gain references by 8. If it is set higher than 1, the value will be used instead of reading high voltage from the scope. |
| 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. |
| NoCameras | Set to 1 if there are no cameras, to avoid trying to connect with any camera in properies. There must still be properties for at least one camera in the properties file, and an ActiveCameraList with at least one camera in it. |
| DummyInstance | Set to 1 to have same effect as using the /DUMMY command line argument, namely allowing a second instance of the progarm to run. |
| 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. The program will print a warning in the log on startup if unicode or other non-standard ASCII characters are placed in this title. Such characters may cause problems in software reading file headers. IMOD seems to work with Unicode, but single-byte characters in the extended character set will cause problems before IMOD 4.11.12 or 4.12.16. |
| GlobalAutodocEntry | Key-value pair to be placed in the global section of the autodoc for any image file with an autodoc: MRC files with associated '.mdoc' file, HDF files, and '.idoc' files. The key is the first word of the entry, an equals sign after the key is optional, and the value is the rest of the line. |
| FrameFileTitle | String to use for one or more additional titles in the header of frame stacks saved for a K2/K3 camera, in a frame mdoc file written to for each stack, and for the frame stack mdoc file that can be written for each set of frames. The entry must be all one line but the entry can specify multiple title lines, separated by '\n' (the backslash is typed in, this is not a newline character). For MRC file headers, the lines will be truncated at 80 characters, and there can be at most 9 lines (or 7 for unnnormalized data). For a TIFF file description entry, these limitations do not apply in the file entry itself, only in the title listing by the IMOD 'header' command. |
| 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. This entry is overridden by a command-line argument specifying a plugin path. Files ending in -32.dll or -64.dll are skipped by 64-bit and 32-bit versions, respectively. |
| PluginPath2 | Additional path from which to load plugins. Loading as described in 'PluginPath' is not affected. Files ending in -32.dll or -64.dll are skipped by 64-bit and 32-bit versions, respectively. |
| PluginPath2-32 | Sets PluginPath2 with this path only if running 32-bit. |
| PluginPath2-64 | Sets PluginPath2 with this path only if running 64-bit. |
| 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. |
| ProgramTitleText | Text to add to the title bar; it will appear after 'SerialEM - ' and before the list of open filenames. |
| ScriptMonospaceFont | Exact name of monospaced font available on the system that should be tried first when using a monospaced font in the script editor. |
| PythonModulePath | Path to directory containing the Python 'serialem' module(s). The default is a directory named PythonModules in the directory containing the SerialEM executable. |
| PathToPython | Version number and path to directory of a Python installation containing 'python.exe'. The version number should start with two digits with a period between them. For Python 3.4 or below (i.e. 2.7), where modules are named 'serialem.pyd' and must be in separate subdirectories, this version string is added to the module path, so it must match the name of the subdirectory, i.e., 3.4-32, 3.4-64, or 2.7 if using the standard package or modules. If you have both 32- and 64-bit installations (e.g., for Python 3.5), you should include '-32' and '-64' on these strings so that the '#!Python' entry at the start of a script can be used to pick which one to run. There can be multiple entries of this property, or none if there is just one Python you wish to use and it is on the system path. |
| PythonIncludePath | List of directories to search for a file to be included in a Python script with '#includeFile'. The current directory will be searched first, then each directory in the list until the file is found. Separate multiple directories with semicolons and do not include any extra spaces before or after a directory. |
| EnableExternalPython | Set to 1 to allow externally run Python scripts to control SerialEM. This property can be set with the 'SetProperty' script command. |
| 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. |
| AssumeDPI | Follow with a DPI value to use in font and dialog scaling instead of the detected one. This enables the program to be scaled independently of the Windows scaling or DPI setting. If you want to scale for 120 DPI, you will also need to set 'DisplayIsNot120DPI 0' |
| 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. When it is 120 DPI, it assumes that this is a Thermo/FEI scope where monitor scaling was set to 120 DPI even though the monitor was probably 96 DPI, and it sets the variable controlled by this property to 1 to prevent the scaling. Set this property to 0 if the display really is 120 DPI (e.g., a laptop screen) and you want the program to scale just as for other DPIs. Setting to 1 will prevent scaling if you enter 120 for the 'AssumeDPI' property. |
| PanelConstants | Follow with three numbers: 0; the extra height to add to control panels; and the extra width to add to control panels. The defaults for height and width are 5, and 8 for DPI < 120, 0, and 0 for DPI = 120, and 6, and 10 for DPI > 120. The first value used to be the title bar height but this is now handled properly. |
| 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, or -1 to prevent Administrator mode from being turned on, which will prevent calibrations from being saved. |
| ShiftScriptOnlyInAdmin | Enable the script editor buttons to shift scripts up and down only if Adminstrator mode is on. |
| DisableOrHideFile | Full path name of a file listing dialog and menu items to be disabled or hidden unconditionally during the run of the program. See Hiding and Disabling Menu and Dialog Items for details. Make sure that the user settings files in use have good values for the items being made inaccessible before adding this entry. |
| BasicModeDisableHideFile | Full path name of a default file listing dialog and menu items to be disabled or hidden when Basic Mode is turned on in the Settings menu. Since the Basic Mode filename is saved in the settings file as of SerialEM 4.1, 30-Nov-22, this entry just provides a default if no Basic Mode file name was read in from settings. If a filename is provided in neither file, the program looks for and reads SEMbasicModeItems.txt in the system directory. See Hiding and Disabling Menu and Dialog Items for details. |
| 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, but it is better to use the menu entry to remove bad calibrations instead, since rotation and pixel size measurements are stored in this file too. |
| 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 if the memory limit described next is less than 5 GB, otherwise it is 1024. |
| 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 of 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. The default is 75% of system memory for 32-bit versions with less than 2.4 GB and for 64-bit versions; for 32-bit versions with more memory, the default is 1.8 GB on a 32-bit system and 3.7 GB on a 64-bit system. |
| ScopeUpdateInterval | The interval in milliseconds between calls to the function that reads scope properties and updates the user interface. The default is 150, raised from 100 on April 10, 2018. For a JEOL, the update function does not normally access the microscope so this should be OK. |
| UpdateDuringAreaChange | Set to 1 to let the scope update routine run, update the display, and respond to changes during a low dose area change. Ths may be fine on Thermo/FEI scopes, but is less likely to be so on JEOL scopes. |
| 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, and providing parameters for CTF fitting. See FFT command help for details. Follow 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, 5, and 0.07). |
| DefaultMaxCtfFitRes | Default maximum resolution for CTF fitting, in Angstroms. This default applies until the user enters a different value, at which point the resolution becomes a user setting. The default value is 5 if the voltage on program startup is > 125, otherwise 10. |
| CtfplotterPath | Full path to Ctfplotter executable, if you are using one in an IMOD or 3dmod package for viewing CTF plots. This entry should not be needed if this directory is in a standard location or on the system path. See Additional Packages for GPU and Python Support, and for Displaying Gnereal and Ctfplotter Graphs for details |
| MinCtfplotterPixel | Minimum pixel size, in nanometers, for images to be sent to Ctfplotter. When fitting an image with a smaller pixel size than this, SerialEM will reduce the image to this pixel size. This both speeds up Ctfplotter, and avoids crashes with versions below 4.12.57, before Ctfplotter itself automatically did an initial cropping to 0.105 nm if it received images with smaller pixel sizes. The default is 0.115 nm. A larger value may be desired if images with smaller pixel sizes are routinely fit. |
| 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. |
| ThicknessCoefficient | Coefficient used for computing ice thickness from the log of the ratio of intensities in unfiltered and energy filtered images, such as by the 'ComputeIceThickness' script command. |
| 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 a Thermo/FEI scope. Thus, use 'SocketServer 1 x.x.x.x' to connect with a Thermo/FEI scope through that server. ID 4 is assigned to the JEOL camera server, 5 is assigned to the Tietz camera remote server, and 6 is assigned to the Hitachi remote shared memory server. ID 7 is assigned to Python scripts run from SerialEM, and ID 8 is assigned to externally run Python, but these should be used only in 'SocketServerPort' entries; there should be no SocketServerIP entry for 7 or 8. |
| SocketServerPort | Socket ID and port number for a server whose address is given in a 'SocketServerIP' entry. The default ports are 48890 for SerialEMCCD, 48892-48895 for Thermo/FEI, 48896 for JEOL camera, 48897 for Tietz, 48898 for Hitachi, 48888 for externally run Python, 48889 for Python scripts run from a primary instance of SerialEM, and 48887 for Python scripts run from a Dummy instance of SerialEM. |
| 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. |
| FEISEMServerIP | IP address of Thermo/FEI scope, for connecting with FEI-SEMServer.exe on the scope. This has the same effect as 'SocketServerIP 1 x.x.x.x'. |
| FEISEMServerPort | Port number of the first port for connecting to FEI-SEMServer.exe on a Thermo/FEI scope. This has the same effect as 'SocketServerPort 1 x.x.x.x'. |
| BackgroundSocketToFEI | Set to 1 to open a fourth socket connection to a Thermo/FEI scope for tilting slowly while acquiring data. |
| SmallFontsBad | Set to 1 if the small fonts, such as in the Camera and Script control panel, are strangely pixelated and unreadable. |
| 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:
|
| SpecialDebugLevel | Set to a number to specify a debug level for special output that can be obtained without all of the items output with DebugOutput 1. Currently 1 for failed JEOL calls, 2 for all calls except from update, and 3 for all calls including update (i.e, like 'J' without all the output from '1') |
| DiscardSettings | Set to 1 to have 'Discard on Exit' in the Settings menu initially turned on. |
| 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. |
| DoseLifetimeInHours | Duration over which dose calibration will be considered valid when starting the program and reading the short-term calibrations file. The default is 24 hours. |
| 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. |
| SuppressSomeMessages | Set to 1 to suppress selected messages, which so far include starting a long-running operation, the operation finished successfully, and setting to standard focus in LM. Items will be added on request. |
| BufferStatusShowFocus | Set to 0 to show magnification instead of defocus in the summary lines of the Buffer Status panel. |
| ExternalTool | Follow with the text of an entry to insert into the Tools menu, which will appear when at least one entry has been created. |
| ToolCommand | Follow with the number of an entry in the Tools menu (numbered from 1) that will be used to run the command, then with a program to run. The program will be started asynchronously; i.e., SerialEM will not wait for it to finish. See The Tools Menu and Running External Commands for a description of the rules governing this command. |
| ToolArguments | Follow with number of a associated entry in the Tools menu (numbered from 1) and then with a list of arguments ot include when running the command. See The Tools Menu and Running External Commands for a description of what can be included in this arguments entry. |
| AllowWindowWithTools | Set to 1 to allow processes run with the Windows CreateProcess function to open a DOS window when using the Windows command processor; the window is suppressed by default. Tools and the script commands RunProcess, CreateProcess, and Ctfplotter use this function. |
| AddDPItoSnapshots | Set to 0 to prevent the pixel size from being stored as a resolution in dots per inch in TIFF snapshots, or to a specific value greater than 1 to set that value as the DPI. The default is 1 to store pixel size. |
| EndIfVersionBelow | Stop reading properties if the integer version number of the program is below the given value. The integer version is 10000 times the first digit, plus 100 times the release number, plus the update value; thus use 30900 to skip properties not defined in version 3.8. More than one entry is allowed; the one for the earlier version should come before the later version. |
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 Thermo/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. |
| UseAPI2ForDE | Set to 1 to connect to the DE server with API 2. This new interface was added in server 2.5, but can only be used with server DE 2.7 or higher. Currently the only advantage of API 2 is that continuous (live) mode works well and can give much higher frames per second. SerialEM cannot switch connection methods after it determines the server version, so this property is the only way to access API 2. The default read port for API 2 is 13240 (see DECameraReadPort). If you change this property after connecting to the server, you will probably need to restart the server. |
| SkipAdvancedScripting | Set to 1 to prevent Thermo/FEI cameras from trying to use the advanced scripting
interface and to prevent attempts to use other functionality in advanced scripting. Set
to a negative value to send a sum of flags about particular components of advanced scripting to skip,
which is necessary if there is no license for them. Flags are: -1 to skip the temperature control component and use the functions in standard scripting -2 to skip the autoloader component and use the functions in standard scripting If AdvancedScripting.dll is installed (Titan 2.9/Talos 1.9) but there is no license for it, the initial connections through this interface work but camera acquisition fails. This property prevents that. |
| 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 non-energy filter camera if that is an energy filter camera. The property 'KeepSTEMstate' will make this selection be ignored if it would cause a change in STEM state. |
| AssumeCameraForDummy | The index on the CameraProperties line of the camera that should be assumed to be the current camera when the program is started with the /DUMMY command line argument. This entry will override 'InitialCurrentCamera' in that case. Low dose parameters will be set to the EFTEM or STEM parameters if appropriate. |
| KeepEFTEMstate | Set to 0 to revert to original program behavior, which was to leave EFTEM state when starting and exiting the program. (Changed for 3.7.6, 6/12/19) With its default of 1, 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 will still switch if necessary 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 energy filter 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. |
| KeepSTEMstate | Set to 1 to stay in or out of STEM on program startup even if 'InitialCurrentCamera' is set with a camera that would require it to change state. |
| AllowCameraInSTEMMode | Set to 1 to keep the program in STEM mode when switching to a true (non-STEM) camera. It will still switch into STEM mode when a STEM camera is selected, or change the selection to a STEM camera when the scope is switched into STEM mode. |
| WarnIfBeamNotOn | Set to 0 to suppress the warning when taking an image with the column valves closed or beam off. |
| 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 a Thermo/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 a 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 a Thermo/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.. If fewer than 4 values are entered, the defaults remain for the rest. |
| 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. If fewer than 4 values are entered, the defaults remain for the rest. |
| RioMinExposures | Minimum exposure times for 4K Rio camera at each binning, in seconds. The defaults are 0.05, 0.0125, 0.0062, 0.0062. Use OneViewLikeMinExposures for 3K and 2K Rio. |
| RioDeltaExposures | Allowed increment in exposure times for 4K Rio camera at each binning, in seconds. The defaults are 0.001, 0.001, 0.001, 0.001. Use OneViewLikeDeltaExposures for 3K and 2K Rio. |
| OneViewLikeMinExposures | Minimum exposure times for any OneView-like camera at each binning, in seconds. Follow with the actual OneViewType value (i.e., 3 for 3K Rio, 4 for 2K Rio) then one or more new values The defaults are 0.0667, 0.0667, 0.0667, 0.0667 for 2K Rio; 0.0667, 0.0167, 0.0167, 0.0167 for 3K Rio; 0.05, 0.0125, 0.0062, 0.0062 for 4K Rio, 0.02, 0.005, 0.005 for ClearView, and 0.0244, 0.00609, 0.00203, 0.00203 for Metro. |
| OneViewLikeDeltaExposures | Allowed increment in exposure times for 4K Rio camera at each binning, in seconds. Follow with the OneViewType value then one or more new values The defaults are 0.001, 0.001, 0.001, 0.001, or 0.00203 for Metro. |
| 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/K3/Alpine 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/K3 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/K3 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). |
| MinimumK3FrameTime | Minimum duration for a frame in Dose Fractionation mode on the K3 camera. The default is 0.01332 sec. |
| 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). |
| K3ReadoutInterval | The interval between readouts on the K3; exposures are constrained to a multiple of this. The default is 0.000666 sec. |
| K3HWDarkRefExposure | Exposure time to use for updating the hardware dark reference on a K3. The default is 10 sec. |
| 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. The default is 12 for K2, or 32 for K3 (if there is not also a K2). |
| EarlyReturnUseSaveThread | Set to 1 to do saving in a separate thread when doing an early return, thus allowing a new acquisition of frames to begin before saving is finished. This entails stacking all the frames in a temporary stack, which is itself a costly step, and testing has not shown any advantage to using a separate thread rather than avoiding the stacking of frames, as is done in the Multiple Record routine and with the #S entry to 'EarlyReturnNextShot'. A thread will not be used when aligning in the plugin or when making tilt sums or using a frame threshold. Also, the thread will not be used if the memory limit controlled by the 'K2MaxRamStackGB' property is not at least twice the size rquired to stack all frames. |
| K2CountingReference | Full path and name of counting mode software gain reference for K2 camera 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 or K3 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. |
| ShowLinearForAlpine | Set to 0 to hide the Operating Mode group box and Linear and Counting radio buttons in the Camera Setup dialog for an Alpine camera, and have that dialog change linear to counting in a selected control set. |
| TestGpuInShrmemframe | Run GPU frame alignment in shrmemframe instead of plugin. |
| Falcon General Properties | |
| FalconReadoutInterval | Value which intermediate frames are constrained to be a multiple of with Falcon camera. The default for Falcon 2 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. The default for Falcon 3 is 0.02495, but at least one site needed 0.02505. The default for Falcon 4 is 0.004021, and the default for Falcon 4i is 0.003133. Do not set this property unless it is needed, and do not use this property if there is more than one kind of Falcon camera, or multiple cameras needing different intervals; use the camera property 'ReadoutInterval' for whichever camera requires a non-standard interval. If you determine a refined value to avoid exposure time adjustments when saving as EER, as described in Adjusting timing for Falcon 4 camera, set the camera property instead. |
| Ceta2ReadoutInterval | Value to which frame times are constrained for a Ceta 2 camera; the default is 0.025. |
| 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 Thermo/FEI software will not write to. For Falcon 2 with new interface or Falcon 3 or 4 or Ceta 2, path to top directory where frames are written by the Thermo/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 or 4 or Ceta 2, 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 or 4 storage server, this entry would typically be 'C:\OffloadData\TemScripting\BM-Falcon'). If there is more than one Falcon or Ceta 2 camera, the camera property 'FalconLocalFramePath' needs to be used instead for all but one of the cameras. |
| FalconReferenceDir | For Falcon 4, path to directory on the storage server containing the EER gain reference; another 'local' path accessible to SerialEM. This entry is also required to do frame alignment in SerialEM or IMOD. (If SerialEM is running on the Falcon 4 storage server, this entry for a Titan would typically be 'C:\OffloadData\ImagesForProcessing\BM-Falcon\300kV') If there is more than one Falcon camera, the camera property 'FalconGainRefDir' needs to be used instead for at least one of the cameras. |
| RotFlipInFalcon3ComFile | Value for the 'SumRotationAndFlip' option placed in Alignframes command files when saving frames from a Falcon 3 with alignment in IMOD. Originally, Falcon 3 frames were saved to MRC files with no metadata that could be used to detect, inversion in Y, so SerialEM uses a value that assumes images also need an inversion. If this gives an incorrect orientation with current Thermo/FEI software versions, set this property with the needed value, which should be the same as the camera's RotationAndFlip property. |
| SubdirsOkInFalcon3Save | By default, SerialEM assumes that the storage server for Falcon 3 can save only to a direct subfolder of the storage location, probably because this the restriction for early versions of Thermo/FEI software. It is possible that more recent software versions allow subfolder trees, since they do for Falcon 4. Set this property to 1 to test whether this is the case. |
| Falcon4CanSaveEER | Set to 0 if a camera is identified as Falcon 4 (FEIcameraType 5) but Advanced Scripting does not support saving EER files (TEM server version less than 7.6, i.e., Titan 3.6, Talos 2.6). You will also need a patch to Advanced Scripting from ThermoFisher to acquire frames. |
| TakeUnbinnedIfSavingEER | Somewhere between server 7.8 and 7.12, the Falcon 4 camera started giving an error when acquiring binned or subarea images and frames are being saved as EER or just aligned in SerialEM. This property controls whether FEIScopePlugin or FEI-SEMserver will request such images unbinned and full sized, and bin and extract the subarea from them in software. It is now on by default; you can set it to 0 to avoid the extra computation if you have an earlier server that does not have the new behavior. |
| 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. |
| CEOSServerIP | IP address of a CEOS filter; this property alone indicates that the system has a CEOS energy filter. The camera(s) on the end of this filter should have the property 'GIF 1'. If you have not used the RPC server before, you must enable it. In the CEOS Panta Rhei Image Viewer, select 'RPC server' in the CEFID menu. When you enable the server, a dialog will pop up with an option to 'Enable on start'. |
| CEOSServerPort | Port for connecting to a CEOS filter; the default is 7081 and this property should not be needed. |
| BiggestGIFApertureNumber | The number of a GIF 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 energy filter (EF) 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 physical chip sizes; e.g. one would use a value of 2 with a 1K 794 before the EF 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 EF and a 2K, 30-micron pixel EF camera. |
| FilterSlitInOutDelay | Delay time in DM ticks (60th of second) with a GIF, or in msec with an omega, Thermo/FEI, or CEOS filter, when inserting or retracting slit. Default is 18; for this and other filter delays, the default is not scaled to be used as msec so default delays are 16 times longer for GIFs. |
| 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 eV. |
| FilterOffsetDelayBase1 | Base delay (in ticks for GIF, msec for Omega, Thermo/FEI, or CEOS 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, Thermo/FEI or CEOS 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 for a GIF 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. For a CEOS filter, set to 1 to set energy loss using only the high tension offset. Otherwise, the liner tube voltage will be used if possible, and high tension offset will be adjusted instead only if setting the energy shift with liner tube voltage would make it go out of range. In either case, the energy shift reported by the program is the sum of high tensin offset and liner tube voltage. It is recommended that the high tension offset be set to -50, and liner tube voltage adjusted to compensate, to avoid transitions between the two methods of setting shift. |
| 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. |
| OmegaCanDoNegativeShift | Set to 1 on a JEOL with omega filter if it allows negative energy shifts or 0 if it does not. The default is 1 if the JeolhasNitrogenClass property is set and 0 if it is not. |
| 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. |
| NoFilterControl | Set to 1 to be able to define a camera as an energy filter camera with the property 'GIF 1' and use EFTEM mode for it although there is no SerialEM control of the filter itself. As of SerialEM 3.9.0 1/28/21, this property is not needed for a Falcon 4 camera with 'GIF 1' set since it is set automatically. |
| UseFilterInTEMMode | Set to 1 to use the filter in TEM mode and prevent switching the microscope into EFTEM or GIF mode when the program's EFTEM mode is set. |
(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 a Thermo/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 a Thermo/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. |
| JeolDetectorID | Use this entry to designate a camera as on-axis or off-axis on a JEOL scope using IS deflectors for image shift. SerialEM will select the detector in the JEOL software when the camera is switched to, causing the scope to apply or remove a stored PLA offset for off-axis cameras. The IDs may be 16 for on-axis and 17 for off-axis. This is untested; use the SetCameraPLAOffset script command for scopes using PLA. |
| 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 STEM camera or -3 for STEM simulator 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 15 or 16 for XF416 non-GPU version 17 or 18 for XF416 GPU version 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. Entries 15 to 18 imply a RestrictedSizeType of 9. |
| AMTcameraType | 1 for an AMT camera. AMT cameras can coexist with Gatan cameras after SerialEM 3.2.3. |
| FEIcameraType | 1 for a Thermo/FEI Eagle camera or Thermo/FEI STEM, 2 for a Falcon 1 or 2 camera, 3 for Ceta 1 or 2 or another camera with no shuttering capabilities, 4 for Falcon 3, 5 for Falcon 4, or 6 for Falcon 4i. If 5 is used for a Falcon 4 and the TEM server version is less than 7.6, you must also set the general property 'Falcon4CanSaveEER 0'. 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 Advanced scripting camera interface is available. 12, 14, 15, and 16 can be used to test various features for Falcon 2-4 with the Advanced scripting interface even when it is not present, if the property 'SimulationMode' is also entered. |
| 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, 4 for a DE_LC1100, or 5 for an Apollo camera. This entry implies RestrictedSizeType 3 for the LC1100 only. |
| K2Type | Set to 1 for a Gatan K2 Summit camera, 2 for a Base camera or for a Summit booted into Base mode, or 3 for a K3 camera. |
| OneViewType | Set to 1 for a OneView camera or 2 for a Rio camera, which will be mapped internally to 3 or 4 for 3K or 2K cameras. Set to 5 for a Metro camera, which is handled like a OneView even though it is similar to a K3. Set to 6 for a ClearView camera. |
| RotationAndFlip | This entry is used for STEM cameras and K2/K3 and Falcon cameras, as well as for DE cameras with a server version of 1.0.1243 or higher. 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/K3 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. In general, it should be set when using frame alignment in SerialEM or IMOD so as to make the aligned image match unaligned ones. For Falcon 2, it is applied to frames being saved, so setting it is optional if alignment is not being used. For Falcon 3, it is needed when aligning images. For Falcon 4, saved MRC frames are in the correct orientation but EER frames are in native orientation, so the setting is needed to make images aligned either with no saving selected or while also saving as EER have the right orientation. For a DE camera, the operation is applied after aligning saved frames; it should match the operation being done to images in the DE server. |
| 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, Direct Electron, or plugin 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/K3, 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. For Tietz F216/F416/F816/XF416 cameras, the first parameter is 1 by default. For a plugin camera, just the first parameter is used to indicate that a continuous mode should be used; the plugin must have the function StopContinuous as well. |
| 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 8 for DigiScan. It is automatically set to 4 for Tietz cameras with 1024-block readout on 1025-pixel boundaries (F416, etc), and set to 9 for a Tietz XF416 camera, which allows sizes of 256, 512, 1024, 2048, 3072, and 4096 starting at any multiple of 256. |
| 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/K3 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 generally a number between 1 and the number of gains available, which is obtained from the camera interface. The default is 2 for XF416, 1 otherwise. For XF416, 2 is high sensitivity mode and 3 is extended dynamic range mode. |
| LowestGainIndex | Minimum value of the gain index. If it is not 1, then the gain index is constrained to be between this number and this number plus the number of gains minus 1. The default is 2 for XF416, 1 otherwise. |
| 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. |
| TietzFlatfieldDir | Full path of directory holding flatfield images saved by the TVIPS software. This entry enables gain normalized image to be obtained from the TVIPS software for F216, F416, and XF416 cameras. |
| SubareasByCropping | For a Tietz camera, set to 1 or 3 to acquire full-sized images and extract subareas by cropping when obtaining normalized images from the TVIPS software, which avoids having to collect subarea flatfields and allows any subarea to be taken with flatfielding in the TVIPS software. For 1, it will do so only for non-continuous mode images; for 3, it will do so for continuous mode images as well. Set to 2 to crop subareas from full-sized images for all non-continuous mode images, or to 4 to do so for all images. The default is 3. |
| DropFramesStartEnd | Number of frames to drop at the start and end of a burst mode (frame) acquisition from a Tietz camera. |
| DMGainReferenceName | The full name of this camera's DM gain reference, including spaces and .dm3 or .dm4, but not the path. For cameras with many reference names, just pick one. If the name is long or has strange characters, the best way to enter this is to right click on the name, select 'Rename', then do Ctrl-C to copy the name. Paste this in to this property and add the extension. |
| FalconLocalFramePath | For Falcon 3 or 4 or Ceta 2, path to top directory where frames are written by the Thermo/FEI software, as seen from the computer running SerialEM. If this property is omitted, the path is taken from the general property 'LocalFalconFramePath'; see that property for details. |
| FalconGainRefDir | For Falcon 4, path to directory on the storage server containing the EER gain reference, as seen from the computer running SerialEM. If this property is omitted, the path is taken from the general property 'FalconReferenceDir'; see that property for details. |
| ReadoutInterval | Readout interval for a specific Falcon camera. Use this property if there is more than one Falcon camera and one or more non-standard intervals need to be used. If the system has both Falcon 3 and Falcon 4 with standard readout intervals (see the general property 'FalconReadoutInterval'), this interval should be assigned correctly by the program and this property should not need to be entered. However, a refined value may be desired to get the expected number of frames from Falcon 4 efficiently (without exposure time adjustment) when saving as EER. See the procedure for assessing the readout interval described in Adjusting timing for Falcon 4 camera. |
| CameraSizeX | Size of camera or maximum number of pixels to acquire in X. NOTE: For a K3 camera, if you set the size in X or Y less than the true size and you do NOT set either 'TopOffset' or 'LeftOffset', you must also have the properties 'XMustBeMultipleOf 32', 'YMustBeMultipleOf 16', and 'CoordsMustBeMultiple 1' so that the subareas will be taken by the camera software. These entries are set internally when either 'TopOffset' or 'LeftOffset is nonzero. |
| CameraSizeY | Size of camera or maximum number of pixels to acquire in Y. |
| LeftOffset | Number of pixels to add to unbinned left and right coordinates for each camera acquisition. If this entry or the next is used, the camera size can be set less than its true size to trim off large borders that are unusable. The sum of 'CameraSizeX' and this entry must be no more than the true camera size in X. This entry must be a multiple of the 'XMustBeMultipleOf' and the maximum binning (and of 32 for a K3). Offsets cannot be entered for Thermo/FEI or Tietz F216/416/816 cameras. |
| TopOffset | Number of pixels to add to unbinned top and bottom coordinates for each camera acquisition. The sum of 'CameraSizeY' and this entry must be no more than the true camera size in Y. This entry must be a multiple of the 'YMustBeMultipleOf' and the maximum binning (and of 16 for a K3). |
| 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. The default is 4. |
| 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. The default is 1. |
| 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 a Thermo/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. For a K3 camera, this is the number of counts per electron in counting mode, which is 32 by design, so the default is 32 and the property is not needed. |
| 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'. |
| UseMinDDDFocusBinning | Set to 1 to apply the minimum binning set with the Focus menu entry Set Min Binning when autofocusing with this camera (this is always applied for direct detectors). |
| 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 Thermo/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 a Thermo/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 physical pixel coordinates numbered from 0 at the top left, and for an image in the same orientation as is displayed in SerialEM. Follow the keyword with the top, left, bottom, and right coordinates of the last good column or row in the image. This entry is needed if gain normalization is being done in SerialEM, or if there are defects at the edge of an unnormalized K2 or K3 image that need to be corrected. |
| UsableAtMag | Specifies the coordinates of the usable area at a particular magnification where the image is partly occluded. Follow with the magnification index and the top, left, bottom, and right coordinates of the last good column or row, in unbinned pixels. The top and bottom entries can be set to 0 to avoid limiting the Y dimension, or the left and right entries can be 0 to avoid limiting X. Each entry with a positive magnification index applies only at one magnification and currently has an effect only when setting up montages through Navigator. Alternatively, you can make one entry with a magnification index of 0 to limit the coordinates at all magnifications. |
| 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 at the left. In this and the next 4 entries, the coordinates need to be in physical pixels in an image at the same orientation as would be displayed in SerialEM. This and the following 4 'Bad' entries are needed to handle defects from Gatan and other cameras if gain normalization is being done in SerialEM, or if unnormalized frames are being saved from a K2 or K3 camera. Defect correction will also be done for DE cameras regardless of whether normalization is done in SerialEM. It will be done for K2 or K3 images if any of these entries exist. For a K2, the correction will use the full list of defects obtained by merging the defects entered here with the list of bad pixels from DigitalMicrograph. |
| BadRows | Specify a list of bad rows that will be replaced in all processed images. List the rows in increasing order using physical pixel coordinates numbered from 0 at the top in an image with the same orientation as is displayed in SerialEM. See notes under 'BadColumns'. |
| 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. See notes under 'BadColumns'. |
| 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. See notes under 'BadColumns'. |
| BadPixels | Specify a list of single pixels needing correction. Each pixel is specified by an X and a Y physical pixel coordinate numbered from 0 at the top left. Multiple pixels (up to 19) can be entered on one line, and an unlimited number of pixels can be entered on multiple lines. See notes under 'BadColumns'. |
| 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; a Thermo/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. If the 'SideMounted' property is also 1, the beam will be blanked when the screen is down as well, unless in Low Dose mode, where it is governed by the checkbox in the low dose panel. 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. For a STEM camera, this property has no effect; it is superceded by the option 'BLANK BEAM in STEM mode' in the STEM Controls panel. |
| 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). |
| StartDelayPerFrame | Amount to add to the startup delay per frame when doing dose fractionation with a K2 or K3 camera; the default is 0.005 sec. |
| 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 OneView and K3 cameras, so enter 1 to enable post-actions for a OneView or K3. |
| 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 a Thermo/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. |
| AddToExposureTime | Amount to add to the specified exposure time, in seconds, to get the proper exposure from the camera. For Falcon 3, the default is 0.013, which is needed at least through server version 6.15 (corresponding to a x.15 version of the software for the particular model line), and probably always will be needed. The test for whether a different value is needed is to see whether a 0.05 sec exposure gives twice as many counts as a 0.025 sec exposure for Falcon 3. If not, try a value of 0 then values between 0 and 0.013. The default for Falcon 4 is half the readout interval (0.002). |
| AddToEERExposure | Amount to add to Falcon 4 exposure time (in addition to 'AddToExposureTime' value) when saving frames as EER (default 0.02 sec). This value should be set to avoid adjustments in the exposure time just prior to taking each image. See the procedure for assessing this property described in Adjusting timing for Falcon 4 camera. |
| 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. |
| PostIntensityTimeout | Delay in seconds between changing intensity and taking an image with this camera when it is the currently active one. This can avoid problems with short exposures taken too soon after an intensity change. |
| 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-energy filter 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 |
| FEIFilterType | Set to 1 to indicate that this camera is on a Selectris filter and that the version of Advanced Scripting supports it. With this property set, the program will set 'AdvancedScriptingVersion' to 4 if it is not explicitly set higher by a property setting.. Do not set this property unless you have a server version of at least 7.8 (Titan 3.8, Talos 2.8) or it will crash SerialEM or FEI-SEMserver when a function is called that does not exist in the current version. |
| 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/K3 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 physical pixel per second, then the corrected dose rate in electrons/physical 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 for K2 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 | For Falcon 3: 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. For K3: Ratio needed to make linear and counting mode images give the same dose rate (electrons per physical pixel per second) for images at the same exposure. The default is 350. |
| Falcon3ScalingPower | This entry does three things. For Falcon 3 with the Advanced Scripting interface, 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'. For a 'dumb' Falcon 3 with the standard scripting interface, it activates a scaling so that images with different exposures do not all have the same counts. Its value is the power of 2 that will be used to scale a 1 sec exposure; it can be between -9 and 18, and its default is again 4. |
| FalconEventScaling | Factor used to scale electron events when frames are aligned from an EER file for a Falcon 4. See the procedure in Measuring Camera Gain. The default is the value of CountsPerElectron. |
| LinearOffset | For a K3 camera, the offset that needs to be subtracted from linear mode images per camera readout. The default is 8192; this number is defined by the algorithm in the software and should not need adjusting. |
| K3CDSLinearRatio | For a K3 camera, ratio of counts in linear mode with correlated double sampling on to counts with it off; the default is 1.5. |
| CanTakeFrames | If taking frames from a particular camera is supported, set to 1 to enable saving frames, 2 to enable aligning frames, or 3 to enable both saving and aligning. However, for a Ceta camera with the speed enhancement option (referred to elsewhere as Ceta 2), set to non-zero to enable frame-saving; whether frame aligning is enabled depends on whether the path to frames is defined with the LocalFalconFramePath general property or with the FalconLocalFramePath camera property. Taking frames with the Ceta 2 also requires that the Advanced Scripting version be identified as high enough; this will require a property 'AdvancedScriptingVersion 4' unless there is a Selectris filter. For a OneView, Rio, or Metro camera, saving and aligning are done through the SEMCCD plugin just as for a K2 or K3 camera. For other cameras, saving and aligning are done within SerialEM. This is the same frame alignment that SerialEM provides for direct detectors, which is suitable for low-dose images and can run on an NVIDIA GPU. If these capabilities are turned on by default for a particular camera, enter 0 to have them not appear in the Camera Setup dialog. The default is 3 for Tietz XF416 and Gatan Metro, and 0 otherwise. |
| FrameTimeDivisors | Values that frame times are constrained to be a multiple of for each binning, for a camera with CanTakeFrames set. Defaults are provided for OneView and Rio cameras; these are the same as the defaults for OneviewMinExposures and RioMinExposures, except the default is 0.0025 for binning 8 for OneView. Otherwise, the default is 0.001. If fewer values are entered than the number of binnings, the result depends on whether defaults is provided for the camera: if they are, the default applies for the rest of the binnings; if not, the last entered numnber is used for the rest of the binnings. |
| MinimumFrameTimes | Shortest allowed frame time for each binning, for a camera with CanTakeFrames set. The default values are the ones entered or provided for FrameTimeDivisors, except for Tietz cameras, where the default is 0.04 for XF416 and 0.1 per 1024 pixels in Y on the sensor for Fx16 cameras. For these cameras, shorter frames can be taken for subareas. |
| 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 a Thermo/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 Thermo/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 a Thermo/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. A plugin camera (including Tietz) may set this value, but a property entry overrides it. |
| AddedFlybackTime | Set to the added flyback time indicated after running the camera timing calibration procedure. On Thermo/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 Thermo/FEI STEM until a Thermo/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. |
| MinMultiChannelBinning | For a multichannel JEOL STEM interface, follow with a list of the binnings to which the acquisition must be restricted for 2, 3, and 4 detectors. For F200, if the CameraSize entries are 4096, this entry would be '2 4 4'. |
| 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. For a JEOL camera or STEM, the index for a camera must be 0 and the index for STEM must be 1. |
| 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 with API 1 and 13240 with API 2. |
| 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. This property no longer works for server version 2.1.15 and higher; all operations should be done in the server. |
| DEImageInvertXAxis | Set to 1 to flip the image around the Y axis after the rotation, if any, specified by DEImageRotation. This property no longer works for server version 2.1.15 and higher. |
| 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 if the server is local ('DECameraServerIP' set to 127.0.0.1) and 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. |
Most of 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.
| 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 Thermo/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 a Thermo/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 (default 1). For JEOLs, the current density scaling in the program was off by a factor of 700 until SerialEM 3.8.0 beta, 5/15/20. The value of 0.059 commonly found in properties files is now converted to a 1. |
| 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 |
| FilamentCurrentScale | Scaling for converting a relative filament current between 0 and 1 to an actual current value; the default is 100. |
| 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. For Krios, the recommended value is 5000-6000. One way to assess the adequacy of a value is to autofocus twice in Low Dose mode after coming out of a lower-magnification View area and see how the drift rate declines. |
| 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. |
| SkipNormalizations | Set to the sum of 1 to skip projector normalization when changing magnification, and 2 to skip condenser normalization when changing spot size, which only happens from a few routines. |
| PostProbeDelay | Time delay in msec after changing TEM probe mode on a Thermo/FEI scope before an exposure starts; default 3000. |
| LowestMModeMagIndex | Index of the lowest magnification in non-LM 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. |
| LowestEFTEMNonLMIndex | Index of the lowest non-LM magnification in EFTEM mode, needed if this is different from LowestMModeMagIndex. The default is LowestMModeMagIndex. Having a different LM-nonLM boundary is not properly handled before SerialEM 4.1, 7/17/22. |
| LowestGIFModeMagIndex | Index of lowest magnification that should be used for tasks with the energy filter camera. The default is to use the LowestEFTEMNonLMIndex (or LowestMModeMagIndex if that is not set). |
| 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, or highest spot size to use, if 'MinSpotSizeToUse' is not 1; default is 11 for Thermo/FEI, 5 for Hitachi and JEOL. |
| NumberOfSTEMSpotSizes | Number of spot sizes in STEM mode; the default is the same as in TEM. |
| MinSpotSizeToUse | Minimum spot size to set from the program; default is 1. |
| IntensityToC2Factor | This entry is no longer needed; instead, the factor is measured by a calibration procedure and stored in the Calibrations file |
| AddToRawIntensity | Amount to add to the intensity values coming back from Thermo/FEI scripting to keep the internal intensity values in the program in the range of 0 to 1; default is 0. |
| ConstantBrightnessInNano | Set to 1 if fringe-free illumination on a Thermo/FEI scope keeps brightness from changing when intensity (C2) changes in nanoprobe. The program will allow dose to be calibrated, will use that dose value at the same spot size regardless of C2 setting, and will use the spot intensity calibration to use a dose calibration at one spot size to obtain the dose at another spot size, again regardless of intensity. |
| 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. Limits of -0.5 and 2.5 should be adequate for initial scope setup. The Illuminated Area Limits calibration should be done early in scope setup; it will supercede this property. If this property is added in the absence of that calibration, 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 Thermo/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. These limits also provide the default coordinates for the polygon that will be fit for a full montage, but a user entry of grid limits in the Navigator - Montaging and Grids submenu will override these default coordinates. If the Navigator is open, a dashed red rectangle defined by these limits is drawn when the image being displayed extends beyond these limits. |
| MaximumTiltAngle | Set to the maximum angle that can be tilted to without generating an error. The default is 60 for Hitachi, 69.9 if 'UseIlluminatedArea' is set; otherwise 79.9. Titan Krios and Halo need the 69.9, hence this default, but Titan 60-300 or Themis allow 80 degrees and custom Grenoble allows 90, so for them the property should be set to 0.1 degree less than the limit. |
| TiltSpeedFactor | Set a default tilting speed factor on systems that support varying the tilt speed, to be applied except when tilting with a specific speed factor. See the description of speed factors for the tiltDuringRecord command. |
| StageXYSpeedFactor | Set a default speed factor for X/Y stage moves on systems that support varying this speed, to be applied except when moving with a specific speed factor. |
| 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.) If this item is set, you will probably also need 'RotateHeaderAngleBy180' set to 1 to preserve handedness in reconstructions from tilt series. |
| StageInvertsZAxis | This property affects the direction of focus and Z height changes when accounting for tilt. It is defaulted to 1 on a Hitachi, where tilting around the Y axis inverts the direction of the Z axis in the 'specimen' coordinate system. |
| 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 is generally needed if InvertStageXAxis is set, and is probably needed for a Hitachi HT7700 or 7800. As of SerialEM 4.0, 10/7/22, this property is set by default if InvertStageXAxis is set; enter a 0 to override this behavior. |
| 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 Thermo/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 a Thermo/FEI scope, this may need to be set to something besides 1 if 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. |
| UseSquareShiftLimits | Set to 1 to test each axis of image shift separately against the limit on image shift, or 0 to convert the whole image shift into distance on the specimen and test that radial distance against the limit (the behavior before SerialEM 4.1). The default is 1 for Hitachi and JEOL scopes, Krios, and other FEI/Thermo scopes with access to advanced scripting. |
| MaxCalibrationImageShift | Maximum image shift change when calibrating image shift |
| MaxLMCalibrationImageShift | Maximum image shift change when calibrating image shift at LM-mode mags. |
| SixPointIScalMinField | Minimum field of view for using a 6-point image shift calibration instead of a 9-image one; the default is 3 microns. The 6-point calibration cannot assess the consistency of drift or account for changes in drift over the course of the calibration, so it is less appropriate for higher magnifications. |
| 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 Thermo/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 Thermo/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 Thermo/FEI scopes, otherwise 40 microns. |
| MaxStageCalExtent | Maximum distance over which to do the stage calibration, unless this distance is less than one-fifth of the camera field size. 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 low mag. At very low mag, the extent will be at least one-fifth of the camera field size up to a fixed limit of 500 microns. 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. |
| StageCalToggleInterval | Interval between toggling images during stage calibration. The default is 250 msec. |
| StageCalNumToggles | Number of times to toggle images during stage calibration. The default is 10. |
| 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 Thermo/FEI and 0.2 micron for JEOL. |
| RestoreStageXYdelay | Delay in milliseconds between tilting and changing X/Y when restoring stage position after tilt; the default is 100 msec. |
| UseTrialSizeForShiftCal | Set to 1 to use the image size, and subarea offset if any, 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 a Thermo/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 energy filter, 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. Entries can be added to
the table for calibrated camera lengths or tilt axis rotation angles.
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 Any line can also have an optional calibrated camera length after the nominal one, which will be used to set the pixel spacing in an image file header and in an associated .mdoc file for images taken at that camera length. After the calibrated camera length, or 0 if one is not available, a tilt axis rotation angle can be added, following the same convention as for RotationAndPixel lines (rotation of tilt axis from the image X axis, counterclockwise positive). 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. A table can also be added on a Thermo/FEI scope by running a script; see List Mags for details. |
| NumberOfCameraLengths | The number of camera lengths in regular diffraction mode and in LAD mode on an Thermo/FEI scope. These numbers are needed for the Mag/CamL spinner in the Microscope Control panel to work right. If a camera length table is entered for a Thermo/FEI scope, this line must be included after the table to reset the number for regular diffraction mode. Otherwise, the defaults are 21 and 22 for Titan and 16 and 21 for other scopes. |
| DiffractionShiftScaling | Scaling applied to convert the step size for beam movement in the Microscope Control panel into the value for diffraction shift used in the call to the microscope plugin. For JEOL scopes, the plugin takes values between -100 and 100, the percent of full scale on the PLA deflector. For Thermo/FEI scopes, the plugin takes milliradians, but the Microscope Control panel also divides the step size by the camera length in meters before applying this scaling factor. The default is 10. |
| 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. By default, they are
also adjusted up or down for camera startup and clearing times lower or higher
than 0.8 seconds (the default for 'StartupForISDelays'). 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 The default with no table entry is a linear delay of 1 sec per micron of movement, which is excessively long for large image shifts. With at least two entries, it will interpolate between them and extrapolate beyond them; with one entry it will use the single delay at all moves. The values originally distributed in properties files through 2021 were: ImageShiftDelays 7 0.1 0. 0.3 0.4 0.8 0.9 1.6 1.7 3. 3. 3.5 3.5 4.0 3.7 If these values are still present and 'ISdelayScaleFactor' still has its default value of 1, the values will be revised based on new measurements from frames in two cases: 1) when a Thermo/FEI scope can be recognized as of a newer generation, namely when either it is a Titan or the program uses Advanced Scripting, the values are changed internally to the new recommended values, listed below, and 'ExtraISdelayPerMagDoubling' is changed to 0.1; or 2) for a JEOL scope, the values are left as they are and 'ISdelayScaleFactor' is set to 0.2. For a Talos or Glacios that can not be recognized because it does not use Advanced Scripting, it is recommended that the table be changed to these values: ImageShiftDelays 4 0.1 0. 0.3 0.4 0.5 0.5 1.0 0.5 When the table is recognized as having these new values and 'ISdelayScaleFactor' is 1, 'ExtraISdelayPerMagDoubling' is changed to 0.1. When the program adjusts values automatically in these 3 cases, it also changes the adjustment for camera startup in 'StartupForISDelays' from 0.8 to 0.25 to reflect the new way that values were measured. To get a message on startup about whether defaults were recognized and values were changed, set 'DebugOutput' to '1' or a letter. |
| 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. The recommended value is 0.2 for JEOL scopes. |
| 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. |
| StartupForISDelays | Startup time involved in the measurement of the 'ImageShiftDelays', the sum of 'StartupDelay' and 'BuiltInSettling' camera properties. The default is 0.8; this should be set to ~0.25 if new delays are entered based on frames. |
| 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). |
| NormCondenserInLowDose | Set to 1 or 2 to change the option in the Low Dose control panel for 'normalize beam through View' to use the microscope call for normalizing lenses instead. With 1, it will normalize condenser lens (C1, C2, C3 if present); with 2, it will normalize the minicondenser and objective lenses as well, in a single call. Such normalization is not available on JEOL. |
| 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 Thermo/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 a Thermo/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 or K3 to retract. |
| CheckPosOnScreenError | For a Thermo/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. |
| HasSimpleOriginSystem | Set to 1 if there is a SimpleOrigin nitrogen filling system. Calls to check dewar status and refill dewars will access this system. For proper function, a first generation system must be running a version of the SimpleOrigin software from August 2021 or later, with the changes added for it to work at University of Texas Medical Branch (UTMB). |
| DewarVacCapabilities | This property determines what operations are supported by the scope management routine configured in the Dewar and Vacuum Management dialog. It is the sum of two flags: 1 if there is an autoloader on an Thermo/FEI scope plus two if there nitrogen filling systems accessible by scripting commands. For a Thermo/FEI scope, the default is 3 for a Krios, 0 otherwise; for a JEOL scope the default is 2 if the JeolHasNitrogenClass property is set. |
| ScopeHasPhasePlate | This property determines whether the 'Condition Phase Plate' task appears in the Navigator Acquire at Items dialog. If necessary, set to 1 if the microscope has a phase plate and a version of scripting that supports moving it. It is defaulted to 1 for Thermo/FEI scopes with Advanced Scripting and for JEOL scopes that have the JeolHasNitrogenClass property set. Set to 0 to omit the task from the dialog when there is no phase plate or no support for moving it. |
| ScopeCanFlashFEG | This property determines whether the 'Flash FEG' task appears in the Navigator Acquire at Items dialog. If necessary, set to 1 if the microscope has a cold FEG and a version of scripting that supports flashing it. The default is 1 for a Thermo/FEI scope identified as having advanced scripting version 4 if it supports flashing, and 1 for a JEOL scope that has the JeolHasNitrogenClass property set. Set to 0 in these cases to omit the task from the dialog. |
| LowDoseChangeAtZeroIS | Set to 1 to have the Low Dose area switching routine zero out image shift before changing areas and restore the previous shift afterwards. |
| 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). |
| NoDefaultPeakErasing | By default, the autoalign routine will try to detect whether the specimen is periodic and erase the peaks in the FFT caused by this periodicity when calibrating image or stage shift. Set to 1 to override this default, in which case the 'Erase periodic peaks in Autoalign' option in the Image Alignment & Focus panel governs whether erasing is attempted. |
| 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 BTID astigmatism calibration and/or correction (default 3.2). A setting made through Focus - Set BTID 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 was 0.1, became 0.04 as of 3.7.6, 6/12/19); '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 BTID coma-free calibration (default 10) and for CTF-based coma-free alignment. A setting made through Focus/Tune - Set CTF Coma-free Params or Focus/Tune - Old Coma-free Alignment - Set Beam Tilt will be retained in the settings file and override this default. The optional 'F' entry is the focus at which BTID 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 BTID astigmatism or coma-free routines (default 500 msec). The optional 'B' is the delay after changing beam tilt for the coma-free routines (default 750 msec); it is applied only if it is larger than the delay set with FocusPostTiltDelay. |
| CtfBasedLDareaDelay | Additional delay after changing low dose area for CTF-based coma-free alignment. The delay is needed to settle out focus changes. The default is 8 seconds. |
| AstigBTBacklashDelay | Delay between first and second setting of beam tilt or stigmators, which are set with backlash in the astigmatism and coma routines and when compensating image shift for beam tilt and astigmatism. A value of 0 makes it skip the backlash step and set the deflectors only once. The default is 100 msec. |
| AdjustForISSkipBacklash | Set to 1 to skip the backlash of beam tilt and stigmators when adjusting for image shift in the Multiple Record routine and various script commands, or 0 to do the backlash. The default is 1 for JEOL scopes, 0 otherwise. |
| SkipAstigAdjustmentForIS | Set to 1 to omit the adjustment of astigmatism when adjusting beam tilt for image shift in the Multiple Record routine and various script commands, even if the calibration of coma versus image shift includes an astigmatism measurement. Set to -1 to omit the adjustment for beam tilt and adjust only astigmatism for image shift; with this setting, the coma vs. image shift calibration will skip the coma measurement, allowing it to be run on Cs-corrected scopes. |
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. |
| MontMaxOverlapFraction | Maximum fraction of overlap allowed in the Montage Setup dialog. The value will be constrained to be between 0.25 and 0.75; the default is 0.5. |
| 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. |
| MontageAutosaveLog | 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 other situations. Default is 5 microns for Thermo/FEI, 10 microns for JEOL, and 20 microns for Hitachi. This entry must be positive; a negative entry makes it use the default. |
| StageRelaxation | Microns of movement to apply opposite to the last stage movement, available in specific situations to reduce drift. Default is 0.025. |
| MontageMinZigzagOverlap | Minimum number of microns of overlap between pieces for doing a stage montage in a zigzag path, in which it goes up a column, down the next column, up the next column, etc. The default is 15. This should be at least 10% of the observed backlash when reversing directions. |
| 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. |
| MontageUseTrialInISRealign | Set to 1 to use the Trial parameters without modification when aligning to an adjacent piece with image shift. Otherwise, the program will reduce the binning and exposure time of Trial to get an image no bigger than a certain size. This option is not appropriate for CCD cameras, but for cameras like the OneView where binning saves little time and it costs time to switch binning. |
| 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-frequency 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. |
| MontageScriptToRun | The number of a script to run after acquiring the image and before saving it, numbered from 1. Values less than 1 will be ignored. The montage will stop with an error if the script tries to run a montage, read from a montage, or do various file operations that would affect the current open file. There are probably other script operations that would interfere with montaging and possible crash the program, so use this with caution and do not assume that the program can do too many different things at once. |
| MontageAllowHQinLD | Set to 1 to allow parameters for high-quality stage montages to be seen and set in Low Dose mode. |
| NoMontXCorrThread | Set to 1 to prevent cross-correlations for piece alignment from being run in a background thread while the next piece is acquired. |
| 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). |
| EucentricityRestoreStageXY | 1 to restore stage X and Y position after each tilt and/or Z change for fine eucentricity only, 2 to restore it for both routines |
| 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). |
| DebugRoughEucentricity | Set to 1 to have each image pair being correlated copied to buffers C, D, etc during coarse eucentricity task. |
| 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). |
| EucentricityMaxFineAngle | Maximum angle to go to in the fine eucentricity task (default 24). |
| EucentricityFineIntervalAtZero | Tilt increment to use at zero tilt in the fine eucentricity task (default 8). Tilt increments vary as the cosine of the angle. The minimum increment for fine eucentricity is controlled by 'WalkUpMinInterval'. The increment used will be somewhat different from the entered value in order to make the tilt steps reach the highest angle with regularly varying intervals. |
| EucentricityFineSubareaMeans | Follow with either a binned size in X and Y or fractions of camera field in X and Y to compute and print to the log the mean in a subarea of that size during the fine eucentricity procedure, adjusted for tilt-foreshortening and for the alignment shift of the image. |
| ZbyGFocusScalings | Follow with pairs of values, a defocus offset and a scaling factor, indicating how to scale an defocus value measured with the given offset into an equivalent Z height change See Extended Autofocus and Non-reciprocity Calibration for Using Eucentricity by Focus for a script to obtain these values. |
| 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 Thermo/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. |
| CookerRealignMinField | Minimum camera field of view, in microns, for the realignment afer running cooking routine. Default is 8.0. |
| NavVisitReturnMinField | Minimum camera field of view, in microns, for the reference image used to realign to the current point after visiting a Navigator point for a special operation (such as phase plate conditioning). Default is 8.0. |
| TiltBacklash | Amount to tilt to eliminate tilt backlash. Default is 3.0. |
| 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 |
| UseTrialSizeForTasks | Set to 1 to use the area defined in the Trial parameter set instead of a full-frame image for various tasks that use a common routine for making the parameter set for tracking shots. The full field size will still be used to evaluate what magnification provides the minimum field of view. |
| 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. |
| RefineZLPLeaveCDSMode | Set to 1 to turn off CDS mode for running Refine ZLP on a K3 camera and turn it back on afterwards. Special settings for K3 are needed with CDS mode until Gatan fixes problems with the initial frame having doubled counts. A good alternative to this setting is to set 'RefineZLPMinimumExposure' to 0.1 sec and 'RefineZLPMaxMeanRatio' higher as needed, such as to 0.1. |
| 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 as of SerialEM 3.6. |
| FindBeamOutsideFrac | Criterion fraction that peripheral regions of image must be below the mean around the centroid for considering them to be outside the beam. The default it 0.15; it needs to be higher if the region outside the beam has excessive residual counts. |
| 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. |
| DistortionMaxMoveToCheck | Maximum stage move in microns to check for whether the shift determined by correlation is close enough to the target; namely if this value is 0 or the stage move is less than this value, it will check and repeat the move if necessary, but if the move is greater than this value it will ignore the measured shift and trust the stage move. |
| 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. |
| ContinuousAlignPairwise | Number of frames to include in pairwise alignment when aligning continuous mode images, or 0 for alignment of each image to a cumulative aligned sum, -1 for alignment of all pairs, or -2 for alignment of pairs among half of the images or at least 7. The default is 0 for maximum speed. |
| ContinuousAlignBinning | Binning to use for alignment when aligning and summing continuous mode images; the default is 4. |
| ContinuousAlignFilter | Cutoff radius of Gaussian filter in unbinned reciprocal pixels when aligning continuous mode images; the default is 0.06. |
| UseGPUforContinuousAlign | Set to 1 to use a GPU for aligning continuous mode images. This property is active only on program startup, not if set with the SetProperty script command. |
| MultiInHoleStartAngle | Angle at which to start the first peripheral image taken by the Multiple Records routine when doing points within a hole. The default is to set this angle to the short axis of the camera unless tilted to 20 degrees or above, in which case it sets the angle along the tilt axis. Enter a value greater than 500 to have it along the tilt axis at any tilt angle, or the actual angle desired, or a value less than -500 to restore the default. |
Tilt series controller properties
| TSDefaultStartAngle |
Default angle for starting and ending tilt series, when controller |
| 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 Thermo/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. |
| TSStepForBidirReturn | Tilt step size for returning to the start angle of a bidirectional series when not using Walk Up. The default is 10 degrees for JEOL scopes, 5 degrees otherwise; enter a large value to return in one step. |
| TSSpeedForOneStepReturn | Speed factor to use when returning to the start angle of a bidirectional series in one step because of a large value for 'TSStepForBidirReturn'. For information about using a speed factor, see the script command TiltDuringRecord. The default is 0 for normal speed. |
| TSRestoreStageXYonTilt | Set to 1 to restore stage X/Y position after tilting during dose-symmetric series only, 2 to do so in all tilt series, or 0 to disable this feature. The default is 1 for Thermo/FEI scopes, 0 otherwise. Restoring the stage position may help with tracking on modern stages and be detrimental on older stages. |
| TSDosymFitPastReversals | Set to 0 to do predictions only based on positions since a tilt direction reversal, 1 to include positions before the reversal for predicting X and Y, or 2 to also include focus values before a reversal when predicting Z. The default is 2. |
| TSDosymBacklashDir | Set to -1 or 1 to have the direction of backlash in dose-symmetric tilting be toward negative or positive tilts, respectively. The default is for the backlash direction to be the same as the first direction of tilting. |
| TSCheckScopeDisturbances | Flags for whether to check and wait for disturbances caused by microscope operations before taking the Record. Enter the sum of 1 to check for dewars being filled on Thermo/FEI and JEOL scopes that support it, and 2 to check for the PVP on a Thermo/FEI scope. The default is 2 on a Thermo/FEI scope, otherwise 0. |
| TSTrackAfterScopeStopTime | Minimum duration of a scope disturbance that will force retracking when resuming after the operation is over. The default is 5 sec. |
| TSFocusAfterScopeStopTime | Minimum duration of a scope disturbance that will force autofocusing when resuming after the operation is over. The default is 120 sec. |
| TSWaitAfterScopeFilling | Extra wait time in seconds after the end of dewar filling when the setting of 'TSCheckScopeDisturbances' causes a wait before taking a Record. The default is 600 (10 minutes) for JEOL and 0 for Thermo/FEI. |
| 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/K3 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. The asynchronous saving will not be done when aligning frames, or when the option for an initial partial sum is set in the setup dialog. |
| 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 selecting a map for Realign to Item, this value plays two roles: 1) Within a montage map, 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. 2) When picking a map for aligning, a map can be selected over one that is better in other ways for several reasons, but the distance to its edge must be bigger than this value. In particular, an anchor map taken at the same position as a higher mag map can be guaranteed to be picked for alignment if half of its shortest side is more 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 0.7 times the size of the smallest objective aperture that might be present during the realign operation, minus a few microns of allowance for error in aperture position. Or, if there is a magnification that you know can be imaged without an aperture intruding, you can set it to a number larger than the maximum of the X and Y sizes of the camera field at that magnification. The default is 15 microns, which is very conservative. |
| 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. Set to a negative value to use the full frame size only when the montage consists of a singe frame in X and Y. |
| MaxMontReuseWaste | The maximum fraction of image area that is extra, or wasted, when a montage fit to a polygon is changed to match the size of a larger, 'reusable', montage file. The ratio of piece area for the original fit to piece area for the reusable file must be bigger than 1 minus this fraction; otherwise the polygon will be assigned to a smaller montage. The default is 0.2. |
| MaxReconnectsInNavAcquire | For JEOL scopes only, set to the maximum number of times to try renewing the connection to the microscope when there is a time out received at the top level in Navigator Acquire at Items (default 0). |
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/K3 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. |
| 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. |
| MinInitializeJEOLDelay | Minimum value for 'InitializeJEOLDelay'; if 'InitializeJEOLDelay' is beow this value a warning will be printed in the log on startup. The default is 5500; set to 0 to disable warning. |
| 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. One way to determine IDs is have 'JeolUpdateByEvent' set to 1 and debug output set to 'e', and insert or retract the screen or other detector. |
| JeolPairedDetectorID | Set this to indicate the ID of a detector that moves in complementary fashion to the one specified by the JeolMainDetectorID. The program will insert this detector when retracting the main one, and vice versa. |
| 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. |
| JeolHasBrightnessZoom | Set to 1 if the version of TemExt.dll supports the BrightnessZoom function, so that the program can disable and re-enable this as appropriate. The function was added between 2015 and 2018. |
| JeolHasNitrogenClass | Set to 1 to enable use of calls for testing and starting nitrogen refill and flashing a cold FEG, or 2 to enable use of calls for getting the nitrogen level and using the autoloader. |
| JeolFlashFegTimeout | Timeout in seconds for flashing the FEG; the default is 45. |
| JeolEmissionTimeout | Timeout in seconds for turning the emission back on after flashing the FEG; the default is 180. |
| JeolHasExtraApertures | Set to 1 to use aperture commands that can specify up to 12 kinds of apertures instead of 6. |
| JeolRelaxationFlags | Flags for the operations after which the program should wait for the scope's lens relaxation to finish on a JEOL: set to the sum of 1 for magnification, 2 for spot size, and 4 for alpha changes. |
| JeolStartRelaxTimeout | Timeout in milliseconds when waiting to see lens relaxation start after a change. The initial placekeeper default is 1000. |
| JeolEndRelaxTimeout | Timeout in milliseconds when waiting to see lens relaxation end after a change. The initial placekeeper default is 10000. |
| JeolLensRelaxProgram | A sequence of lens changes to normalize or relax them using free lens control. Using
a procedure developed by Mike Strauss, each lens is stepped
in a negative direction by half the given amplitude, stepped in a positive direction
by the full amplitude, then stepped back to its original value. Each program has
a normalization index when determines where it is used in the program. Follow with: Normalization index: 1 for spot, 2 for condenser, 3 for objective, 4 for projector, 5 for a condenser group used for NormalizeAll with flag 1, and 6 for a projector group used for NormalizeAll with flag 2. Number of steps in the positive direction. Delay after each step (can certainly be 0 if multiple changes are interleaved). Lens number #1: lens numbers for FLC calls are: 0: CL1, 2: CL3, 6: OL Coarse, 7: OL Fine, 8: OM, I0: IL1, 11: IL2, 12: IL3, 13: IL4, 14: PL1, 15 or 16: PL2, 19: FL Coarse, 20: FL Fine, 21: FL Ratio. Amplitude #1: size of change in positive direction. Changes should generally be under 0.05. Follow with up to 5 more lens number and amplitude pairs. On a 3200, a good entry for a condenser normalization that includes IL1 is: 2 10 0 0 0.002 2 0.005 10 0.00 |
| RelaxLensesSequentially | Set to 1 to have a sequence of changes specified with 'JeolLensRelaxProgram' done completely for one lens at a time, instead of interleaving the changes. |
| NumberOfAlphas | Set to the number of alpha settings available; the default is 3. |
| 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. |
| JeolExternalMagDelay | Delay time in msec before the periodic update routine responds fully to a mag change not imposed by SerialEM. When multiple mag changes occur, newer microscopes (CryoARM, F200) generate errors if SerialEM tries to restore image shift too soon. The default is 0, values around 1000 may be needed. |
| 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. Decrease the value to increase the movement. Changing this will invalidate existing beam shift calibrations; use 'BeamShiftCalAlphaFactors' if you need a different scaling for an alpha after calibrating at another alpha. |
| 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. |
| BeamShiftCalAlphaFactors | Amount by which to scale the initial spot movement when calibrating beam shift for different alpha values. Enter values for the alphas in order starting with alpha 1; values are not needed for all alphas and the default is 1. On a 2200, factors of 10, 2, and 1 are appropriate. |
| BeamShiftBoundaries | Set of magnification indexes at which the beam shift calibration changes substantially. Each index should be that of the higher magnification at the boundary. When there is a beam shift calibration on each side of a boundary (but not necessarily right at the boundary), the calibration used for a given magnification will be the one on the same side of the boundary as that magnification, not the one at the nearest calibrated magnification. The program will allow multiple calibrations separated by these boundaries, even if they are not separated by an image shift boundary. |
| 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. |
| SkipJeolNeutralCheck | Set to 1 to skip the checks for the validity of the neutral IS values, which by default occur once at each mag. |
| 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. |
| NoScopeControlOnStartup | Set to 1 to keep the Scope Control panel closed on program startup, which works around a bug in JEOL software that stops the beam from turning on when this panel is open and the state of the beam switch is being accessed. |
| JeolBeamRampupTimeout | Set a time in seconds after turning on the beam during which the state of the beam switch will not be accessed, to work around th same JEOL bug. |
| 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, or 2 to use ISF, the same coils used for HC mode. |
| HitachiDoesBSforISflags | Flags indicating in which magnification modes the Hitachi scope does beam shift when an image shift is applied, so that SerialEM will not do the beam shift: the sum of 1 for HC mode, 2 for HR mode, 4 for LM 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, namely the area of the screen in square cm. The default is 150. Set to 0 if the current readout does not work. |
| 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. |
| 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 Thermo/FEI, first for nanoprobe then for microprobe. |
| LowestMicroSTEMmag | On a Thermo/FEI, the index of the lowest microprobe magnification, as output by List Mags in the Calibration menu. |
| FeiSTEMprobeModeInLM | On a Thermo/FEI, this property determines how probe mode is treated in LM. With it set to 1 or 2, it will internally consider the mode to be nanoprobe or microprobe, respectively, magnification indexes will be set picked in the respective range of the magnification table, and calibrations will be stored and accessed under those mag indexes. With the default of 0, the internal mode will stay the same as the mode from which LM was entered, and calibrations need to be available in that mode. |
| 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 Thermo/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 Thermo/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 Thermo/FEI and 250 for JEOL. |
| RamperWaitForBlank | With a Thermo/FEI scope, set to 1 if the blanking starts after the beginning of the scan (below the top of the image) when doing the camera timing calibration to measure flyback times. With this set, the program will wait for the Focus Ramper to finish blanking the beam before starting the acquisition. |
| 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 STEM detectors that do not work together; follow with the index 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 index numbers (all numbered from 0). |
| DetectorBlocks | On a JEOL, use this entry to indicate that a STEM detector with a JEOL ID blocks one or more other STEM detectors when inserted. Follow with the detector index of the one that blocks, and the indexes of one or more detectors that are blocked. |
| ScreenInIfDetectorOut | On a JEOL, use this entry if the screen blocks a STEM detector and either that detector or the screen must be in to block the beam from hitting a camera below. Follow with the index of the detector in SerialEM, numbered from 0. Set LowerScreenForSTEM to 0 since the screen cannot be unconditionally raised or lowered in STEM. |
| 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). |
| CameraSetsShareChannelList | Set to 1 to force camera parameter sets for STEM to have the same list of selected detectors. When the selection is changed in the Camera Setup dialog for one parameter set, it is copied to any other set that does not have the same detectors selected, possibly in a different order. This is needed if the STEM system cannot reliably change detectors without intervention. |
| ShotTimeToInsertDetector | Exposure time for the dummy image acquisition needed to insert detectors after entering STEM mode with Thermo/FEI STEM. The default is 3 sec. |
| DigiScanExtraShotDelay | 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, or every time it switches into STEM, 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-filter 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. |
| PartialScanThreshold | Minimum exposure time for displaying partial scans as a STEM image is acquired, for situations that support this (currently just the Tietz scan generator). The default is 0.5 sec. |
| TietzScanCoordRange | Range of internal coordinates to use with the Tietz scan generator. The coordinates have a full range of 65535 and SerialEM can use a range up to 42000 to allow for rotations of up to 45 degrees. The default is 18500, which should give an image size comparable to that with the native STEM on most scopes. Changing this value will invalidate calibrations. |
| InvertTietzScan | Set to 1 if the Tietz scan generator gives an image that is flipped, not just rotated, relative to the viewing screen and other cameras. Changing this property will invalidate calibrations. |