File Properties Dialog
This dialog box provides options for file storage. Most of them have to do with how to treat unsigned 16-bit integer data, produced by 16-bit cameras. The MRC standard used to be that MRC files in integer mode stored data as signed integers, ranging from -32768 to 32767. However, 16-bit cameras have the potential to produce numbers higher than 32767. SerialEM provides five (!) options for dealing with this possibility.
Independent of these choices of how to treat the numeric values, this box provides three options for the format of the file in which data can be saved.
When saving to an MRC file, the dialog provides another option for saving metadata, into a file in the autodoc format. This file will be given the full name of the image stack plus the extension '.mdoc', which stands for 'metadata autodoc'. When you open or read from an existing MRC file, the program will automatically search for an associated '.mdoc' file and read metadata from the file whenever reading an image, thus restoring more information about the image (e.g., defocus) than would otherwise be available.
Both kinds of autodoc files, image and metadata, contain identical information about each image. The files also have information at the top that replicates some of the information that would appear in an MRC header. This includes the 'Pixel spacing', which is the pixel size in Angstroms. The IMOD programs extracttilts and extractpieces can extract the same information from either type of file as they can from the extended header of the MRC file. In fact, they will automatically look for information in an associated autodoc file if the values are not found in the extended header. In addition, newstack and edmont can transfer information from the autodoc file associated with an input file to a new autodoc for an output file.
Save data as:
Allows data to be saved as bytes or 16-bit integers. If there is a 16-bit camera and values are not being divided by 2, or if there are any buffers with unsigned data in them, an option to save in the non-standard unsigned integer mode is also available.
When saving 16-bit data:
Controls the treatment of unsigned 16-bit integer data being saved to a signed integer file. The three options are to truncate at 32767, divide by 2, or subtract 32768, as described above.
Percentage of pixels to truncate converting to bytes:
Controls the fraction of pixels that will be truncated as black (0) or white (255) when images are scaled to bytes.
Images are captured as 16-bit integers, and the default is to save them to file in this mode. Images can be saved as bytes (range 0 to 255), but this requires scaling of the intensity values into this limited range. To keep the scaling from being dominated by a few extreme values (e.g., from X-rays), which would compress the dynamic range for the rest of the image data, the program will find a scaling which truncates a certain percentage of extremely dark and light pixels at 0 and 255, respectively. Every image is scaled independently.
If you select byte storage or saving to a TIFF file with JPEG compression, you can control the fraction of pixels that will be truncated with these text boxes. Your entries here will be saved in your settings file, and separate values are maintained for saving a single image with the Save Single/Save to Other command versus other situations. However, if the data are very noisy and the image is large, you may find that the contrast is poor when viewing a zoomed-down image that was saved as bytes, and that increasing these truncation values does not help much. The solution is to reduce the image before saving, using the Reduce Image command in the Process menu or the ReduceImage script command.
Save in extended header:
Select whether to save tilt angle, C2 intensity value, stage position, magnification, or dose in the header. The dose is referred to as 'exposure dose' because it is the dose incurred during the time when the camera is exposed to the beam, excluding any pre-exposure of the specimen. All of these values can be extracted from an MRC file with the IMOD program extracttilts (use 'extracttilts -h' to see options). Regardless of which items are selected, all of these values and more can be saved in a metadata autodoc file.
Maximum number of sections:
Indicate maximum number of sections that space is needed for.
The program can store various information for each picture in the 'extended header' of the MRC image file. The check boxes allow you to choose which information is stored; namely tilt angles, the stage position, and magnification. If you are montaging, piece coordinates are automatically stored in the header as well. Because these data are placed in the header, the program needs to know when first opening the file how much space to allocate for it. This is the reason for the text box where you specify 'Maximum number of sections'. The admonition is to be generous because if you run out of header space your only choice is to start a new file.
Save extra information in a '.mdoc' metadata file:
Select this option to have metadata saved in a text file with the name of the image file and extension '.mdoc', as described above. When a montage file is opened and the range of coordinates is too large to store in the extended header, a '.mdoc' file is created automatically.
Save images to:
Select whether to save data in an MRC file, a TIFF file holding a single image (not always available), or a series of TIFF files listed in an autodoc file, as explained above. When you select the latter option, the file chooser for specifying the file will attach the extension '.adoc' if you type in a root name without an extension. Thus, the autodoc will be named rootname.adoc, and the TIFF files will be named rootnameNNNN.tif, where 'NNNN' is a 4-digit number starting with 0000. Your selection here will be saved in the settings file when saving a single image with the Save Single/Save to Other command in the File menu.
Type of compression in TIFF file:
Select whether TIFF files will be saved with no compression, the type of compression used in Zip and PNG files, LZW (Lempel-Ziv-Welch) compression, or JPEG compression. ZIP and LZW are both loss-less compression methods that may not save much space. JPEG compression does lose a small amount of information but can save much more space. Your selection here will be saved in your settings file, and separate values are maintained for saving a single image with the Save Single/Save to Other command versus other situations. In contrast, the default values for most other options in this dialog are controlled by entries in the SerialEMproperties.txt file.
Skip this dialog (turn skipping off in the File menu):
Select this option to avoid seeing this dialog every time you open a new file. Instead, existing values will be used. With this option selected, the dialog will open once per session of the program. When you want to see this dialog again, you can turn off Skip File Properties Dlg in the File menu.
Cancel file setup (and montaging, if setting that up).