File menu commands

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.
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.
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.
Continuous Save Toggles saving to file after each line of output to log window.
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.

Open New command (File menu)

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. The newly opened file becomes the current file for reading and writing. The current file can be selected with a spin button in the Buffer Control Panel. The name of the current file is always displayed in the program's title bar

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

Open Old command (File menu)

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.

Close command (File menu)

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.

Save A command (File menu)

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.

Overwrite command (File menu)

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.

Read command (File menu)

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.

Open Log command (File menu)

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).

Save Log command (File menu)

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.

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.

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.

Exit command (File menu)

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