Metrology refinement

Indexing requires highly precise knowledge of pixel positions in laboratory space. Due to the physics of the CS-PAD detector and the brevity of the incident XFEL pulses, a parallelized integrating detector was necessary to build to be able to operate at the framing rates available at the LCLS. 64 asics are arranged in a tetragonal pattern, 2 asics per sensor, 8 sensors per quadrant and 4 quadrants per detector. The placement of these tiles in physical space is measured by the beamline operators optically using electron microscopy. The four quadrants are movable at CXI, necessitating pixel-level adjustments to individual quadrants. cctbx.xfel then refines tile positions to whole pixel, and then sub-pixel precision by calculating spot positions on a highly diffracting dataset and refining tile locations versus actual spot positions for each tile. This creates four levels of metrology information and corrections. These levels and the method of measuring and refining them are detailed below.

Of the operations of cctbx.xfel, calculating and refining metrology is the operation most suited to beam line staff and the authors of the software. Please don't hesitate to ask for assistance regarding any aspect of this procedure.

Optical Metrology

LCLS provides initial tile placements. Periodically the detector is disassembled and re-built, necessitating new calibration information. The optical measurements are included in the cctbx.xfel in the source code and are reference by your pyana config file. See [preparatory steps] for more information.

Quadrant positioning

The CXI CS-PAD detectors have quadrants on rails to allow re-sizing of the central hole. The second-level of metrology corrections consists of unit pixel corrections to entire quadrants using the cxi.view quadrant calibration tool. First, create a virtual powder pattern using averaging (see [preparatory steps]). Usually the standard deviation or maximum projection will show virtual powder ring. An image with strong rings to moderate resolution is desired. Once obtained, start the calibration tool with this command:

cxi.view <virtual powder pattern image path> viewer.calibrate_silver=true distl.detector_format_version="CXI 7.1"

Note, the flag distl.detector_format_version is a legacy requirement that will be phased out.

Once loaded, you will see your image and many red rings, incidentally corresponding to the diffraction pattern of silver behenate. Additionally, a separate settings panel will be present with 8 input boxes corresponding to the x and y offsets of each of the four quadrants, UL, UR, LL, and LR (upper and lower, left and right). Manually adjust the offsets until the powder rings are circular through the whole image, using the red rings as guides. These corrections will but put into your phil parameters file in the distl quad_translations entry in this form:

distl {
  quad_translations =  2 -6  3 -6 -7  0 -1 -4
}

Where the numbers are listed in this order: ULX ULY, URX URY, LLX LLY, LRX, LRY