X-ray centering at MAX IV (in production)

[anamga]

This is a description of the automated X-ray centering procedure current in use at MAX IV. It is both used by users doing "interactive" data collection and during automated data collection. Interactive users can select to the X-ray centering when they save a grid. For automated data collection, X-ray centering is compulsory and immediately follows optical loop alignment. However, the procedure is the same in both cases:

1. Doing a 2-D grid scan at an initial omega orientation
2. Processing of the 2-D scan images to determine an optimal point
3. Translating the sample to that point and rotating omega by 90 degrees
4. Doing a line scan, processing the images to determining a 3-D point.
5. Moving the crystal to the point

Input:

• Grid cell : Defaults to the current beam size (defined by the MD3 aperture). Interactive users can change this to the value they want. For automated data collection we force it to 10 microns.
• Grid lines, columns and position and initial omega. Interactive users can choose the sample orientation and draw the grid. In automated data collection we use predetermined values for the grid size; the position is based on the results of the preceding automated loop centering.
• Line scan length: based on the 2-D grid definition
• Exposure time, beam transmission. Interactive users can choose these values specifically for the 2-D grid scan. For automated data collection the exposure time and transmission are based on the input diffraction plan. Defaults are 10 ms exposure per frame and 100% transmission. The corresponding values for the line scan are always set automatically based on the values chosen for the 2D scan.
• Resolution: Interactive users can choose the value when they set up the 3D scan. For automated data collection, the value is defined in the diffraction plan. The default is the value at the current energy and detector to sample distance.
• Energy: Users can set the value, interactively or (in automated data collection) in the diffraction plan. Defaults to the current value.
• Delta omega: Defined automatically (an oscillation is needed to trigger the detector)

Output: Currently, a single 3-D point based on the results of the dozor analysis

[disussionnotifier[bot]]

@mxcube/automation-udc-and-queue A new discussion was created in the "Automation/UDC and Queue" category: #1125

[anamga]

Some improvement we would like to implement in the future:

• Modify or replace the current autoloop centering program to determine the area to scan based on the shape of the loop. We would like to look into using Murko for this.

• Improve image analysis after the grid scan to be able to estimate the size and shape of the crystals and detect multiple samples (using indexing results can be useful for this). Replace the orthogonal line scan we currently do by a 2nd grid scan to explore better the sample morphology

• Output an estimate of the crystal(s) size in addition to the center

[rhfogh]

Compared to my original post, these goals would suggest the following changes:

• Having the centring procedure return a list of crystal positions instead of a single position.

• For each position adding a description of the crystal 3D size and shape - format to be determined.