3 Intermediate Frame Mode with SerialEM

Currently, Falcon camera can output frames at rate about 17~18 frames per seconds. If one defines a very long exposure, the camera system can generate many frames. However, possibly due to the limitation of computational power of Tecnai XP computer, the maximum numbers of chunks can be saved to disk drive is 7, for any single exposure. In the world of SerialEM, they are called frame and sub-frame, equivalent to FEI's term - chunk and frame. Which frame containing which sub-frames are defined by an XML file. From Tecnai User Interface, one has to edit this file manually, which is annoying.

SerialEM tries to work around this. Put following three lines to general section of your property file.

MaxFalconFrames         7
FalconFrameConfigFile   C:\tecnai\data\Falcon\IntermediateConfig.xml
LocalFalconFramePath    C:\Temp\Falcon-dump

SerialEM tries to simplify user input by using a frame selector dialog window which can be lauched from Camera Parameter Setup window, as shown below.

When the check box next to "Intermediate Frame Saving is ON in FEI dialog", then the button below it "Setup Frames to Save" becomes clickable. Clicking on this button will bring up a frame selector dialog window, as shown below.

This frame selector dialog window makes our life a lot easier!

The frames/chunks written to harddrive are in format of raw, 4-bytes integer, with 49 bytes header. They can be viewed via TIA interface, by clicking "View in TIA" on Falcon Intermediate Image Tool window and then select the file.

SerialEM can stack the series of raw frames together to a single MRC stack file, with 16-bit as default. Therefore, it is recommended because it takes less diskspace. This stacking process writes frames to stack and deletes the frames, one by one. SerialEM can even take a few exposure and combine all the frames into a single MRC stack. This has to be done from macro command.


The above macro will make three exposure and output a single MRC stack file.