Leginon

h1. 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 an small off-axis scintillator-coupled light-sensitive CMOS survey camera.

h2. Camera behavior differences

|property|traditional CCD|DE-12|

|number of readout ports|1 to 4 for 4k camera|number of columns on sensor|

|allowed exposure time interval|1 ms or less|multiple of frame rate|

|minimal exposure time|beam shutter limited (~ 5 ms)|frame rate limited (~25 ms @ 40 frames/s)|

h2. Camera Settings for DE-12

!de12camera_settings.png!

* *Exposure time*: total sensor readout time(?). *DE-12 software rounds up the time to next valid readout time that is multiple of frame rate*.

* *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 sensor signal readout.

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.

h3. More about Exposure Time:

Because DE-12 software may modify the actual exposure time, if a time is used for preset, it should be confirmed by sending the preset to scope/camera and have it send from the camera/scope again.  The returned value is the true value.

h3. More about sensor readout delay

DE-12 uses a rolling shutter that minimizes dead time between frames.  However,as a result, 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 their need*.

* 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 scale down (i.e.,divided by number of frames) to single frames in the raw frame moving stack making.

* To catch onset of the beam, apply a negative  sensor readout delay.

* If  need to use DE-12 for low-mag MSI imaging, use a slight positive readout delay to couple with minimal exposure time and camera binning.  Compare the intensity of the image at different readout delay to choose the appropriate value. Without positive readout delay, the minimal exposure image would have low signal-to-noise ratio and strong gradient.  Too much delay may damage the specimen more than acceptable.

h2.  Leginon Functions

The functions can be performed in version 2.2 include:

 * [[DDD summed image acquisition|Acquiring summed frame image thru Leginon]]

 * [[DDD raw frame saving|Triggering raw frame saving]]

 * [[DDD raw frame file transfer|Transferring raw frame images]] off solide-state drive of DE-12 during data collection to a network drive.

 * [[Make DE-12 movie stack|Compiling corrected movie stack]] with Appion using bright and dark images acquired in Leginon