Direct Electron DE-12 direct detection device support¶

CMOS-based direct detection device (DDD) is a new generation of digital camera that can be used with electron microscope. We currently support DE-12 from Direct Electron which is a retractable camera with also an off-axis small scintillator-coupled light-sensitive CMOS survey camera.

Camera behavior difference¶

Camera Settings for DE-12¶

• Save raw frames check box: Determines whether all raw frame images within the exposure time are saved or discarded.
• Frames to use: Frame numbers listed in a tuple to be summed up and saved by Leginon which will be displayed in web image viewer.
• Readout delay: The difference in time between beam-blank shutter opening and start of signal readout. Because DE-12 uses a rolling shutter, the first row is read a full frame earlier than the last row in a given frame.

Camera Settings for frame-saving camera like DE-12 have option that are meaningless for traditional CCD. In the example camera settings shown above, we set the camera to read out at 25 frames per second, i.e., 40 ms per frame determined by MicroManager program provided by Direct Electron before starting Leginon. At this fixed rate, the 400 ms exposure time corresponds to 10 frames. In this example, the summed image returned to Leginon only contains frames 0 to 4, while all 10 frames are saved as raw frames on DE12 computer. In addition, we set -40 ms readout delay so that the readout starts 40 ms before beam-blank shutter is opened.

DE-12 uses rolling shutter. Therefore, the first row is read almost one frame before the last row inside a given frame of readout. If the beam shutter is opened at the same time as the start of the sensor readout, a gradient of intensity would be seen in the first frame. Users should adjust the readout delay according to the need. For example, it is best to apply enough positive readout delay for bright image acquisition to achieve uniform intensity even in the first frame since it will be used to be scaled to single frames in the raw frame moving stack making.

Leginon Functions¶

The functions can be performed in version 2.2 include:

• Acquiring summed frame image thru Leginon
• Triggering raw frame saving
• Transferring raw frame images off solide-state drive of DE-12 during data collection to a network drive.
• Compiling corrected movie stack with Appion using bright and dark images acquired in Leginon