The File menu contains commands for opening, writing to, and reading from MRC image files, and for saving a Log Window:
| Open New | Opens a new MRC file for saving single-frame images. |
| Open Old | Opens an existing image file. |
| New Montage | Opens a new file for saving montaged images |
| Montage Setup | Starts dialog for setting montage parameters. |
| Close | Closes an open image file. |
| Close | Closes all open image files if none are protected. |
| Save A | Saves image in Buffer A to file. |
| Save Active | Saves image in active window to file. |
| Overwrite | Saves image, overwriting a section in the file. |
| Save Single/Save to Other | Saves image in active window to a single-image file other than the open image file. |
| Set Truncation | Sets the amount of data that will be truncated if data are saved as bytes. |
| Set 16-bit Policy | Sets how 16-bit data will be treated when saved to file. |
| Set Signed Policy | Sets how signed data are treated when saved to unsigned mode file. |
| Skip File Properties Dlg | Toggles option to use existing options and skip file properties dialog. |
| Read | Reads an image from a file. |
| Read from Other | Reads an image from a file other than the open file. |
| Read Piece | Reads one piece from a montaged image file. |
| Log Window | |
| Open Log | Opens a log window to record program messages. |
| Save Log | Saves the log window to a file. |
| Save Log As | Saves the log window to a different file. |
| Read & Append | Reads from an existing log file and appends output to it. |
| Save & Autosave Log | Saves the log window to a file immediately and keeps it up to date thereafter. |
| Autoprune Log Window | Removes lines from the log window after saving them to file to prevent slowdown. |
| Use RTF Format to Save | Saves log as an RTF file, preserving color and style. |
| Continuous Save | Toggles saving to file after each line of output to log window. |
| Use Monospaced Font | Toggles using a fixed pitch font in the log windows. |
| Reset Log Position | Makes the log window visible and moves it to the upper left corner. |
| Open Secondary Log | Opens a different log window, either an empty window or with an exsiting log read into it. |
| Save Secondary Log | Saves the last secondary log window that had focus. |
| Set Current Directory... | Opens chooser for selecting the current working directory. | Open .mdoc for Frames | Opens a file for saving metadata about saved camera movie frames |
| Close Frames .mdoc | Closes the metadata file for saved movie frames |
| Exit | Exits SerialEM. |
Use this command to open a new file for saving single-frame images. You will first encounter the File Properties dialog (unless the option to skip this dialog is selected), then the standard Save As dialog box. If the file already exists, you will be asked to confirm that you want to replace it. If you are saving to an MRC file, the extension .mrc will be added automatically unless you put the extension on yourself, use an extension known to the system, or use the extension '.st' or '.map'. (In other words, if you enter 'file.st' it will not make the name be 'file.st.mrc'.)
You do not need to open a file before saving; if you choose the save command before a file is open you will go through the same sequences of steps to open a file.
You can use this command to open a new image file even if another file is already open. Up to 100 files can be opened. The newly opened file becomes the current file for reading and writing. The current file can be selected with the combo box in the Buffer Control Panel. The names of open files are always displayed in the program's title bar, with the current file name enclosed in brackets.
You can open an existing image file for reading and writing with the Open Old command. You can also read from a file without opening it, using the Read from Other command.
Shortcut Key:CTRL+N
Use this command to open an existing image file for reading images from and saving images to. You will enter the File Open dialog box to select a file. If the file is a montage, then montaging will be activated. You can use this command to open a file even when another file is open. The file that you open becomes the current file for reading and writing.
Shortcut Key:CTRL+O
New Montage command (File menu)
Use this command to open a new MRC file for saving montages. You first enter the Montage Setup dialog box, which allows you to specify the number of frames, magnification, and binning. From there, you enter the File Properties dialog box (unless the option to skip this dialog is selected) then the Save As dialog box. A new montage can be started even when there is already an open file; the new file becomes the current open file and montaging is activated with the parameters for this file.
Montage Setup command (File menu)
Use this command to open a file for montaging, or to check parameters if the current open file is a montage. In either case, you first enter the Montage Setup dialog box. If you are starting a new file, you then enter the File Properties dialog box (unless the option to skip this dialog is selected) then the Save As dialog box.
Use this command to close the current open image file. If there is more than one file open, the file with the next lower number becomes the new current file. Montaging may be turned on, or terminated, depending on the type of that file.
Close All Files command (File menu)
Use this command to close all open image files. This command is disabled if any open file is marked as 'protected', such as when a tilt series is running.
Use this command to save the image in Buffer A to the current open image file. If there is no image file open yet, you will first enter the File Properties (unless the option to skip this dialog is selected) and Save As dialog boxes to specify a file. This file will become the open image file, available for further saving. However, only images of the same size can be saved in the same file.
Shortcut Key:CTRL+S
Save Active command (File menu)
Use this command to save the image in the active buffer to the current open image file. If the main window is active, then the buffer currently displayed in the main window will be saved. If some other window is active (has the input focus, with its title bar highlighted rather than gray), then its image will be saved.
If there is no image file open yet, you will first enter the File Properties (unless the option to skip this dialog is selected) and Save As dialog boxes to specify a file. This file will become the current open image file, available for further saving.
Use this command to overwrite an existing image in the current open image file with the image in Buffer A. You will be prompted to enter the number of the section that you wish to overwrite; the default value offered to you is the number of the last section in the file. Sections are numbered from 0.
If you are montaging and need to overwrite a section, you will need to change the current Z value in the Montage Control Panel. However, if a montage was partially acquired with stage movement and the program can resume it, then you can use this command (which appears as 'Overwrite Pieces') to specify the number of pieces to be acquired again and overwritten in the file when resuming the montage.
Save Single / Save to Other command (File menu)
Use this command to save the active image into a new file just for this one image. The file will be left closed when you are done. You will enter the File Properties and Save As dialog boxes, as usual, unless the option to skip the properties dialog is selected. If you specify an existing file, it will be replaced. The menu item is 'Save Single' when there is no open file and 'Save to Other' when there is an open file, to indicate that the file is different from the open file. The selection of file properties are stored separately for files opened through this command and files opened in other ways. The type of file to store, and the TIFF compression type, are saved between sessions. For example, if you choose to store single images as TIFF with JPEG compression, and then select a different compression for saving as a series of TIFFs, single images would still be saved as TIFF-JPEG without having to reselect that in the properties dialog.
Set Truncation command (File menu)
Use this command to modify the truncation of the data when saving images as bytes. When one chooses to save bytes, then SerialEM can avoid compressing the dynamic range of the data by truncating the values of a relatively few pixels. The number of pixels to truncate at the black and white end of the range is initially specified in the File Properties dialog, but can be changed thereafter with this command. Using this command sets the values for the current open file and the default for newly opened files but does not affect any other open files.
Set 16-bit Policy command (File menu)
Use this command to modify the way that data from a 16-bit camera will be treated when they are saved as integers in a signed data file. You will be asked to enter 0 to truncate the data at 32,767, which could give saturated images; 1 to divide the data by 2, which will discard probably useless precision; or 2 to subtract 32768, which will preserve the data in its entirety at the expense of having negative numbers. If a file is reopened, this is the way to set the treatment of the data to be different from the default. Using this command sets the policy for the current open file and the default for newly opened files but does not affect any other open files.
Set Signed Policy command (File menu)
Use this command to modify the way that signed data are saved to a file that is in unsigned 16-bit integer mode. By default positive values are saved without modification, and negative values are truncated at zero. Enter 1 to have 32768 added before values are saved, which will preserve negative values. Using this command sets the policy for the current open file and the default for newly opened files but does not affect any other open files.
Skip File Properties Dlg command (File menu)
Use this command to control whether the File Properties dialog opens when opening a new file. With the option selected, the dialog will open only the first time during a session of the program. Thereafter, the existing file properties will be used when opening a new file. The option can be toggled either here or in the dialog itself.
Use this command to read an image from a file. If there is a currently open file, the image will be read from it; otherwise, you will enter the File Open dialog box to select a file. In that case, the file will not remain open after reading from it. Also, in that case the file can be a TIFF or DigitalMicrograph (dm3) file as well as an MRC file or autodoc (adoc) file.
Unless there is only a single section in the file, you will be asked to enter the section number to read; the default value offered to you is the number of the last section in the file. Sections are numbered from 0.
If you are reading from the currently open file and there is more than one section in it, the Read Current File dialog box will open to allow you to select the section. This box can be left open so that it is convenient to read several images.
If you are reading from a regular file with single frames, the image will be read into the buffer selected in the Buffer Control Panel. If the file that you are reading from is a montage, then SerialEM will read the entire section and leave a binned-down overview in that buffer as well as in Buffer B; it also leaves a full-scale image of the center of the area in Buffer A.
Shortcut Key:Shift+R
Read from Other command (File menu)
Use this command to read an image from a file other than the currently open image file. You will enter the File Open dialog box to select a file. The file can be a TIFF or DigitalMicrograph (dm3) file as well as an MRC file. Then, unless there is only a single section in the file, you will be asked to enter the section number to read; the default value offered to you is the number of the last section in the file. Sections are numbered from 0.
The image will be read into the buffer selected in the Buffer Control Panel unless the file is a montage, in which case SerialEM will read the entire section and leave a binned-down overview in Buffer B and a full-scale image of the center of the area in Buffer A. It is possible to read from a montaged file even if montaging is currently activated with a different file open.
Read Piece command (File menu)
Use this command to read in a single frame (piece) from an open montaged image file. Unless there is only a single section in the file, you will be asked to enter the section number to read; the default value offered to you is the number of the last section in the file. Sections are numbered from zero.
After specifying the section, you will be asked to enter the number of the piece in X and Y; pieces are numbered from 1. The image will be read into the buffer selected in the Buffer Control Panel.
Use this command to open a Log Window for recording messages from the program. Once the window is open, some messages will be logged there instead of presented in message boxes. You can control how much output goes to the window by selecting Verbose in various menus (Focus, Tasks, Tilt Series). Adding text to this window becomes progressively slower the more it contains, which can significantly slow down long-term acquisition that writes to the log. The program will thus periodically prune the beginning of the text in the window after saving it to file. See Autoprune Log Window for details.
Use this command to save the contents of the Log Window to a file. You will enter the Save As dialog box to specify the file, which will have the default extension .log. Once the window has been saved, selecting this command will save it again to the same file as the last time that it was saved.
Save Log As command (File menu)
Use this command to save the contents of the Log Window to a different file from one already specified. You will enter the Save As dialog box to specify the file, which will have the default extension .log. Once you save to a file with this command, using the Save Log command will save to this file.
Read & Append command (File menu)
Use this command to append the contents of the Log Window to an existing log file. You will enter the File Open dialog box to select a file. The program will then read in the contents of this file, place it before any text already in the Log Window, then write the window back out to the file. If pruning has already happened, you will be warned that pruned lines will not be included and asked if you want to continue. You will be able to choose either an RTF or a plain text file. If you choose an RTF fle, any formatting of the existing log will be lost upon saving, even though it may appear to be present in the window. To minimize this loss, use this command immediately after starting.
Save & Autosave Log command (File menu)
When this command is toggled on, the program will save the log to a file immediately and then save it every minute if it has changed. If no file is defined yet, a file chooser dialog will open with a default name based on the date and time. If this setting is already on when starting the program, the chooser dialog will open with that default name at the end of the startup actions. If the log window is closed and reopened, the chooser dialog will come up to define a name at the next autosave, provided that the program is not busy. This will not happen if the log is kept closed.
Autoprune Log Window command (File menu)
Use this command to set the amount of text that will be retained in the Log Window when the program prunes text from the beginning of the window. Pruning keeps the program from running progressively slower as more text is added to the log. Enter the minimum number of lines to be left in the window if lines average 40 characters each. If lines are shorter than 40, on average, then more will be kept. You can enter 0 instead to disable pruning. Internally, the pruning is based on the number of characters in the window. Pruning occurs when the number of characters reaches twice the minimum. Lines are pruned to the half-way point and written to a file. If a log file has not been defined yet, they are written to a file 'AUTOPRUNETEMP.log' in the system directory (the one with properties and calibrations files). When saving to a selected file, pruned lines are copied from this temporary file to the new file. Similarly, pruned lines are copied when using Save As to save to a different file. After pruning, the first line in the window will show the file that the pruned lines can be found in. Pruning will not occur when the log is being saved as RTF, so this command is disabled when saving as RTF is selected and still possible.
Use RTF Format to Save command (File menu)
Use this command to select whether the log is saved as plain text or in an RTF file, which will preserve colors and styles like bolding. Do not use RTF for a log that will grow to over 10,000 lines in an extended acquisition. Pruning is not possible with RTF files, and adding lines to the log will take progressively longer for larger logs. RTF files would be suitable for running batch tilt series when every series gets its own log. The format may also be unsuitable even for shorter logs if Save & Autosave Log is set, because RTF files have to be written entirely each time, whereas new lines are appended to plain text logs. If a log window has already been pruned, it cannot be saved as RTF and will be saved as plain text despite this setting. Conversely, if you start saving an RTF file and then unselect this option, the existing file will continue to be saved as RTF.
Continuous Save command (File menu)
Use this command to control whether each line of output to the Log Window is saved immediately to a log file. If there is no log file open when you turn this on, you will be prompted to open one the next time output is sent to the log window. This command is primarily for debugging purposes and could slow down program operation.
Use Monospaced Font command (File menu)
Use this command to control whether text is displayed in the log window with a monospaced (fixed width) font or a proportionally spaced font.
Reset Log Position command (File menu)
Use this command to make the log window visible in the upper left corner of the display with its current size, or a minimum size if that size if smaller than the minimum.
Open Secondary Log command (File menu)
Use this command to open a secondary log window. The program will first ask if you want to read in an existing log file. If you answer Yes, a file chooser will open for specifying the file to read in. Otherwise, you will be asked for a name to place in the title bar, and an empty window will open. Secondary logs are distinguishable by having a pale yellow background and 'SECONDARY Log:' in the title bar plus this name or the name of the file read in. If a file is already open in a secondary log, selecting it again will just raise to existing log to the foreground. Secondary logs were added to provide a way to view logs conveniently from the Multiple Grid Operations dialog. There is currently no ability to save to a different file, no protection against closing a log with unsaved changes, and no script access to these logs. Such functionality can be added if needed.
Save Secondary Log command (File menu)
Use this command to save a secondary log window. It operates on the last log window that had focus, so click on the desired log window before selecting the menu item. If the window contains a log that was read to a file or has already been saved to a file, it will simply be saved back to that file. Otherwise, a file chooser will open for specifying the file to save into. After saving, the title bar will show the name of that file.
Set Current Directory command (File menu)
Use this command to select a new current working directory, which will become the directory where file choosers open as well as where files will be created or looked for by script commands when no path is specified. A directory chooser will open.
Open .mdoc for Frames command (File menu)
Use this command to open a metadata autodoc file (.mdoc file) for saving information about every set of frames saved from a direct detector camera. The information will be virtually identical to that saved in the .mdoc file associated with an image file. This .mdoc file allows one to preserve information about saved frames without having to save the summed image in SerialEM into a file. The file will be opened every time new data are saved and closed again after saving, so it is always up to date. By setting the general property 'FrameMdocForFalcon', it is also possible to save metadata about acquisitions from a Falcon camera where frames are captured by connecting to the internal frame transfer.
Close Frames .mdoc command (File menu)
Use this command to close the file opened for saving metadata about saved frames with the previous command; more precisely, to stop saving metadata to this file.
Use this command to end your SerialEM session. You can also use the Close command on the application Control menu. SerialEM prompts you to save a log window with unsaved changes or to save settings if you do not have an open settings file.
Shortcuts
Mouse:Double-click the application's Control menu button.
Keys:ALT+F4