Direct Electron Server Reference Maker Dialog

This dialog is used to acquire dark and gain references for normalization of images in the Direct Electron server.  The server itself manages all of the multiple acquisitions and summing operations required.  The server keeps track of references separately for different settings of the frames per second (FPS).  This dialog allows you to set the essential parameters for all of the kinds of references needed; i.e. 6 kinds when electron counting is available and otherwise 2 kinds.  The exposure time and the number of acquisitions are stored separately for each kind of reference.  There is no intrinsic distinction between a linear and counting dark reference or between a linear and pre-counting gain reference other than the FPS used.  The dialog has all these different options to facilitate acquisitions when different FPS's are used for the two modes, but there is no need to take both kinds if the two modes have the same FPS.

When run from a Setup button in the Navigator Acquire at Items dialog box, the dialog is opened in a restricted mode where you can see and change the settings for acquiring a dark reference with the current Record parameters.  Specifically, it will be set for a dark reference with the current Record operating mode and Record settings for using hardware binning and a hardware ROI rather than for the options selected when this dialog was last run, and the latter selections will not be changed after closing the dialog from this mode.

Type of Processing: Linear - Pre-counting - Post-counting

When electron counting is available, this set of radio buttons in included to allow you to make all of the needed references.  Select Linear to make dark or gain references using the current FPS set for Linear mode.  Select Pre-counting to make such references using the current FPS for counting mode.  There is nothing intrinsically different between these references except for the FPS, so if you do not have different FPS values for the two modes, separate references are not needed.  Select Post-counting to make a gain reference to apply after electron counting at native resolution, and Super-resolution to make a reference for super-resolution counting images.

Type of Reference: Dark - Gain

Select whether to make a dark or a gain reference; only a gain reference can be made if Post-counting or Super-resolution is selected.  For DE server version 2.5 and higher, 'Gain' is disabled because the gain reference procedure should be done in the DE interface.

Frames per Second

This text box shows the FPS at which the reference will be taken.  If electron counting is available, it allows you to set the FPS here instead of in the Camera Setup dialog.  If you change the setting here, it will become the current FPS for acquisitions in the given mode.

With hardware binning by 2

This checkbox appears if hardware binning is available; hardware binning will be used if it is selected.  The reference collected will be valid only with hardware binning selected in the Record parameters.

Use hardware ROI with current Record subarea

This checkbox appears if hardware ROI (region of interest or subarea readout) is available.  Subarea acquired will be whatever is currently selected for the Record parameters in the Camera Setup dialog.  Thus, the subarea needs to be set there first, and this option is disabled if there is no subarea set. The reference collected will be valid only with hardware ROI and this same subarea selected in the Record parameters.

Exposure time

Enter the exposure time to use for each individual image to be acquired by the server.  For DE server version 2.5 and higher, this entry is disabled because the server automatically does 10 repeats with this version of SerialEM.

Number of acquisitions

Enter or use the spin button to select the number of individual images to take and average in the server.

When you press the Yes button, the program will initiate the acquisitions; the status bar will show the number done.  If you press Cancel, parameter changes will be discarded.


Press this button to start the acquisition of the reference.

Save & Close

Press this button to close the dialog without acquiring a reference, but saving all parameter changes that have been made.


Press this button to close the dialog without saving parameter changes, with one exception.  If you change the FPS and switch between linear and counting modes, the new FPS value is stored as the FPS for that mode when you leave the mode.