Using Gatan K2 Summit in Leginon » History » Revision 2
Revision 1 (Anchi Cheng, 05/29/2013 03:33 PM) → Revision 2/31 (Anchi Cheng, 05/29/2013 04:57 PM)
h1. Using Gatan K2 Summit in Counting mode in Leginon If you want to use DM's dose fractionation, activate the "save frames" check box in the particular preset camera configuration. You can also use DM's frame alignment algorithm by activating "align frames" check box, but the latter is not recommended since the alignment in DM will delay the return of the image to Leginon and therefore affects throughput greatly. h2. Configuration # Make sure your camera configuration is set to [[Leginon image orientation]] and instruments.cfg matches that resulting orientation and dimension. # This is likely 270 degree rotated with a flip. New version of DM can acquire its internal darkware gain references in this configuration. # K2's dose fractionation (frame saving) only works with full camera dimension without binning. # K2 interface in DM restricts the exposure time to multiple of some set number, depending on the mode. When you enter in DM an invalid number, it automatically change it to the valid one when you click the acquire button. pyscope/dmsem.py has hard-coded values for these precision. Compare them to the precision of the DM version you have since it may change with DM version. # K2 frame exposure time is adjustable in Leginon gui. However, you need to check if the number is acceptable by DM. h2. Preset Recommendation See [[Pre-MSI_Set-up#Preset-Design-Example-for-small-pixel-Gatan K2 camera alone]] h2. Calibrations Most calibration and operation are similar to that of a typical digital camera. Leginon treats linear/counted/super-resolution modes of K2 Summit as three cameras. Therefore, they each need its own calibrations. A python script is available to make the copying of the calibrations easier. See message#1498. You may need to modify it for different modes you are copying calibrations to. h2. Gain/Dark Correction Handling Leginon receives images from DM without software gain correction. This means gain correction is still needed in Leginon. means: h3. h2. Counted/Super-Resolution # The hardware correction has been applied in DM before counting. Therefore, the "raw" image Leginon get are integers and roughly gain corrected. # The dark image in Leginon should always be 0. Therefore, this need only be done once and no need to average several images in In linear mode, the making. # The bright image acquired in Correction node should be taken at the intended exposure time such as 4-5 s, and a large number of images should be used to get an average image. This will account for variation in sensitivity of the pixels. There is likely a general gradient across the detector. * movie frames recorded in dose-fractionation or frame-saving mode are "raw". Appion will use the bright/dark/correction plan of the image transferred to Leginon to make corrected frame during DD Frame Stack making. h3. Linear # The dark image will have a large mean and the value changes with exposure time. Ideally, the dark images should therefore be taken at the same exposure time as the later images to be corrected. Leginon can account for small differences but not a full range. # To avoid saturation by In counted/super-resolution modes, the accumulated hardware correction has been applied, the "raw" image Leginon get are integers, and the dark current, long exposure in linear mode is not recommended. 0.5 s is typical. image should always be 0. # Do not use frame saving with linear mode. The bright image is for correcting variation in sensor response. It is not worth while. This should be taken at long exposure h2. Operation # Typical frame saving preset parameters: 0.2 s frame exposure time, 4-5 s total exposure time at 8-10 e/pixel/s (Some argue that 5 e/pixel/s is better). # Because of its small size, we have a modified [[MSI_Quick-start_for_DD_only|Quick-start procedure]] we use regularly at NRAMM FEI F20. # /myami/rawtransfer.py should be run on We have also a script for transferring the file server frame images from the Gatan computer to transfer the raw frames as it is produced. Leginon's session image path using rsync. See [[DDD_raw_frame_file_transfer]]. K2 frames are saved as mrc stacks. # See [[appion:Direct_Detector_Frame_Processing]] for tools used for processing This will remove also the frames. # To gain correct and align transferred files on Gatan computer so that more images can be acquired automatically. If you choose to only "align frames" but not "save frames", this script delete the frames, start parallel instances of Appion makeDDRawFrameStack.py See [[appion:GainDark correction of the raw frame with or frames generated by DM without drift correction]]. transferring them. h2. Clean up Frame saving generates a lot of files during acquisition and during processing. # Another python script in leginon directory "cleanddraw.py" can help you clean up the transferred raw frames when you start to run out of disk space, too. See Feature #1784 for more details. Here are some notes on odd things that we have to do: # Make sure your camera configuration is set to [[Leginon image orientation]] and instruments.cfg matches that resulting orientation and dimension. # Selective removal of aligned frame stack We use DM's hardware Dark/Gain correction in Appion runs counted and super-resolution mode. DM will only give usable dark reference when the camera is unflipped and unrotated. Therefore, it is necessary to switch between flip/rotate and unflip/unrotate to maintain [[Leginon image orientation]] convention and preparing dark/gain reference in DM, respectively. Many new users forget to switch at first and need reminder several times. # You will still need to be written. do gain/dark correction in Leginon to correct in DM so called software correction. WIthout it, the image of long exposure shows artifact even in counted and supre-resolution mode. # K2's dose fractionation only works with full camera dimension without binning. # K2 interface in DM restricts the exposure time to multiple of some set number, depending on the mode. When you enter in DM an invalid number, it automatically change it to the valid one when you click the acquire button. pyscope/dmsem.py has hard-coded values for these precision. Compare them to the precision of the DM version you have since it may change. # K2 frame save frame rate is currently hard-coded in pyscope/dmsem.py as the variable self.dosefrac_frame_time = 0.200. You may change this number to get different frame time.