Filter Control Panel

This panel contains options for controlling the Gatan Imaging Filter (GIF), a Thermo/FEI Selectris filter, or JEOL omega filter, and the magnification and intensity settings of the scope when operating the energy filter. On the JEOL with omega filter, the option related to camera selection, pixel size, and intensity are not needed and will not appear.

EFTEM Mode (Thermo/FEI or JEOL with GIF only)

The button will toggle EFTEM mode on and off on a Thermo/FEI scope. When EFTEM mode is turned on and the screen is up, the microscope will be placed in one of the EFTEM magnifications. If the screen is down, the microscope will stay at a regular magnification if the 'Regular mag with screen down' option is selected.

For a JEOL with a GIF, the state of the button will reflect whether the program detects that the scope is in GIF mode.  Beyond that, its behavior depends on whether SerialEM can directly detect and control GIF mode on the JEOL, which was a new capability in SerialEM 3.6.  If it can control GIF mode, the button will be enabled; if it can only detect but not control GIF mode, the button will remain disabled.  If it cannot directly detect GIF mode, then it cannot determine the state when in low magnification mode, so this button is enabled in LM mode.  In that situation, it is up to the user to toggle this button if GIF mode is switched on or off in LM mode.

Refine ZLP

This button will start a procedure for refining the alignment of the zero-loss peak (ZLP). The procedure will use a slit of 20 eV, start at the current alignment, and take pictures at progressively lower energies in 2 eV steps until the edge of the slit is moved past the ZLP. It will generally work only if the ZLP is already roughly aligned (within about 15 eV). If it fails to detect the peak, it will try additional iterations with the starting position shifted left or right by the slit width (except in Low Dose mode, where it gives up right away to conserve dose). Pictures are taken with the Trial parameters in normal mode or with the Preview parameters in Low Dose mode, except that the routine will try to lower the exposure by a factor of 10 and double the binning. A small existing energy loss setting in the filter parameters will be taken as a starting position for the procedure and set to zero at the end. This will occur automatically if the loss is less than half of the slit width setting in this panel; if the loss is more than half but still less than the slit width setting, the routine will ask whether you want to take the loss as a starting pointing. The slit must be in for the loss to be treated in this way. In Low Dose mode, the routine will look first at the properties of the current area, if it has the slit in, then examine the properties of the Record area.

If the procedure fails to detect the ZLP, you may need to set or adjust the property RefineZLPMaxMeanRatio.  Run Set Debug Output in the Calibration menu and enter 'F' to see output from the procedure (or turn on Administrator mode in SerialEM 3.7.3 or earlier).  The second column shows the mean counts and the third column shows the difference in mean counts from the previous step, referred to as the delta.  The procedure finds the ZLP when the mean falls below the biggest mean value by the RefineZLPMaxMeanRatio, which is 0.02 by default, and the delta falls below the biggest delta value by 0.1.  However, these two criteria are allowed to trade off against each other, so if the delta falls by much more than 0.1, the mean does not need to fall by as much as the criterion mean ratio. Because of this, you will not need to raise RefineZLPMaxMeanRatio to exceed the minimum ratio of mean to biggest mean that you see in the output.  Try raising the ratio by 0.02-0.03; repeat if necessary.

Adjust Slit Offset (JEOL with no negative energy shift)

If the filter allows only positive energy shifts, then several program features will not work unless the slit is centered with an energy loss sufficiently far from zero. These include the procedure for refining the ZLP, the ability to apply magnification-dependent changes in the energy shift, and the procedure for calibrating the mag-dependent shifts. This button will facilitate adjusting the slit position so that it is centered on the ZLP with a positive energy offset. After you press it, enter the desired offset and press OK. The filter will be placed into spectroscopy mode with the slit in, allowing you to center the slit on the energy-shifted peak. After you make this adjustment, press OK. You should then be able to run the Refine ZLP routine to get the ZLP aligned as well as it would be on a post-column filter.

TEM mode with screen down (Thermo/FEI scope, or JEOL with control of GIF only)

This button determines whether you see an image at normal magnification in TEM mode or in the EFTEM reduced magnification when the screen is down. The normal magnification provided by this option is almost always preferable when directly viewing a phosphor screen.  If you want to check the size or centering of the beam directly in EFTEM mode, or align the crossover correction at lower magnification, you would turn this option off.  When there is a magnified display of the screen, e.g., on a FluCam, the option has much less value; it does allow you to see what is in the field of view at a given magnification. 

Filter (slit in)

Select this option to insert the slit and acquire energy-filtered images. The check box will also reflect the current state of the slit when other programs modify it. When the slit is inserted, the specified energy loss (either zero or the amount in the 'Loss' text box), plus the mag-dependent energy shift, if any, is used to set the filter's energy shift. If the slit is not inserted, then energy shift is maintained at zero.

Slit width

Enter a width in electron volts into the text box, or use the spin buttons to increase or decrease the width by 5 eV. The slit is set to this width regardless of whether it is inserted or not.

Zero loss

Once filtered imaging is selected, you can filter at either zero loss or a specific energy loss. This check box allows you switch easily between the two. With the box checked, images will be taken of the zero loss peak. With the box unchecked, images will be taken at the energy loss specified in the 'Loss' text box.


For filtered imaging, enter an energy loss in electron volts into the text box, or use the spin buttons to increase or decrease the loss by 1 eV.

Adjustment readout

This text shows the energy shift that will be applied to compensate for ZLP alignment changes and also for magnification and slit width changes if the 'Do mag-dependent energy shifts' option is selected. The value is set to zero when SerialEM detects that you have aligned the zero loss peak through DigitalMicrograph or the Thermo/FEI interface, it changes by the calibrated amount of mag-dependent energy shift when you change magnification, it changes by half of any change in slit width that you make if the slit does not open around its center, and it changes by the amount determined by the Refine ZLP procedure. When 'Do mag-dependent energy shifts' is not selected, only the latter changes should affect it.  On a JEOL, the adjustment will include the offset imposed to keep energy shifts positive. The factors determining the adjustment value will be retained for up to 1 hour between sessions of the program, so you should be able to exit and restart without needing to realign the ZLP.

Net offset readout

This text shows the energy shift currently being applied. It should be zero when the slit is not inserted, and the sum of your selected energy loss and the adjustments being applied when the slit is inserted. It should match the value for spectrum offset or energy shift in a Thermo/FEI scope EFTEM panel and is intended to reduce confusion when you see a non-zero number over there.

Clear Adjustment (post-column filter only)

Set the underlying energy shift adjustment to zero and make this effective at the current magnification and slit width, just as when the program detects that the zero loss peak was aligned by DigitalMicrograph.  This button is useful if you align the ZLP before starting SerialEM, and then SerialEM uses an inappropriate adjustment value from a previous run.  If necessary, return to the magnification and slit width at which the ZLP was aligned before pressing the button.

Match pixel size (post-column filter only)

Select this option to have the program adjust the magnification to minimize the change in pixel size when switching between EFTEM and regular magnifications. If the option is not selected, you can get some rather large changes in magnification because the EFTEM and regular lens programs do not match up very well. This feature is not active in low dose mode, where magnifications are defined as part of each exposure area.

Match intensity (post-column filter only)

Select this option to have the program change beam intensity when switching between regular and EFTEM magnifications, so as to maintain a constant electron flux per camera pixel. With this option active, you can set the beam to give a particular screen current with the screen down, and get a predictable exposure level when you raise the screen. This option and 'Match pixel size' can be selected independently, and will operate independently. This feature is disabled in low dose mode because intensities are defined as part of each exposure area.

Do mag-dependent energy shifts

If this option is selected, the program will adjust energy shift to keep the slit centered on a desired energy loss when magnification or slit width is changed. In order for this to work correctly, mag-dependent energy shifts need to be calibrated and SerialEM needs to be aware of when the ZLP is aligned.

Refine ZLP with Trial in Low Dose (post-column filter only)

Select this option to have the Refine ZLP procedure use images in the Trial area instead of the Record area when in Low Dose mode.  The Trial camera parameters will be used with some modifications, such as a 3-fold reduction in exposure time.  You should run the routine with and without this option to verify that there is not a significant dependence of the ZLP on image shift.  The option is disabled for JEOL microcopes because of such a dependency.

Switch cameras automatically (post-column filter only)

With this option selected, the program will automatically select the energy filter or upper camera when EFTEM mode is turned on or off, and it turns EFTEM mode on or off depending on which camera is selected. To protect the upper camera from the intense beam in EFTEM mode, this option is enabled only in Administrator mode.