SerialEM allows convenient use of an energy filter (post-column or omega filter) and efficient tilt series acquisition with filtering. For Thermo/FEI scopes, it relies on the EFTEM software being installed. On JEOL scopes, it works with an omega filter or with a post-column GIF, where it recognizes the GIF mode and may be able to control it. It provides a number of additional features when used with a post-column filter.
Even without SerialEM, there are numerous ways to control filter settings: the EFTEM panel in the Thermo/FEI Microscope User Interface (MUI), the Autofilter palette in DigitalMicrograph, and the Filter Control program in GMS 1 or its equivalent dialog in DM in GMS 2-3. SerialEM tries to be a good citizen among this crowd and respond to changes made in other interfaces. The recommendation from Thermo/FEI was (and may still be) that the filter be controlled only through the MUI. This is probably sound advice for any actions that cannot be done through SerialEM. Specifically, this includes aligning the zero loss peak (ZLP), tuning the EF, and performing spectroscopy.
The biggest problem in using the EF for tilt series is that there may be an energy shift when changing to lower magnifications for various alignment tasks. If the slit is in, the zero loss peak may shift out of the energy range of the slit, and the task will fail. One solution would be to remove the slit when going to lower magnification, but this would cause an unpredictable and potentially large increase in intensity that could saturate the camera. The solution in SerialEM is to calibrate the energy shifts and apply these automatically when changing magnifications, so that the slit can be left in and will still be centered at the lower magnification. The program will also apply energy offsets to accommodate changes in slit width on older GIFs. These capabilities allow you to explore different magnifications and slit widths without having to align the ZLP repeatedly. repeatedly.
SerialEM implements the three standard imaging modes: unfiltered (with the slit out), filtered to record only zero-loss electrons, and filtered to record electrons with a specific range of energy losses. Once filtering is selected, it is possible to switch between zero-loss and a specific energy loss simply by toggling the 'Zero loss' checkbox; however, if you want a different slit width in the two cases you need to adjust it each time you switch between them. See Filter Control panel for more details.
The Filter Control Panel in SerialEM includes a button to refine the alignment of the ZLP. The procedure is referred to as a refinement because it will work only if the ZLP is already close to aligned, say within 10 eV. The Align ZLP function available in other interfaces must be used for initial alignment, because it is capable of finding the ZLP from many eV away. However, the refine ZLP procedure will align the ZLP even when it is a very small fraction of the total electrons, because it concentrates on the drop in signal as the slit is moved off of the left edge of the ZLP. Thus, once a thick specimen is in, the refine ZLP procedure may be more reliable than the Align ZLP procedure run from elsewhere.
Steps for Using a GIF on a Thermo/FEI Scope