Scripts reference

This section contains the reference and usage information for the scripts provided by the TomoAlign package.

Script auto_focus.py

Script to automatically focus the microscope/camera setup at TOMCAT.

For more information, display the script’s help text

auto_focus.py -h

Examples:

  • Run a completely automatic autofocussing procedure:

    auto_focus.py

  • Run an autofocussing procedure with a specified step size of 0.5 microns over a range of +/- 35 microns around the start position at 2430 um:

    auto_focus.py -s 0.5 -r 35 -p 2430

Script find_focus.py

Script to perform an automatic focus search at the TOMCAT beamline.

For more information, display the script’s help text

find_focus.py -h

Examples:

  • Perform a completely automatic focus search:

    find_focus.py

  • Perform a focus search with a set of specified step sizes:

    find_focus.py -s "100,10,1"

  • Perform a search starting at a position of 1800, using a specific set of step sizes and overshoot values, and setting a limit of 3200 for the highest search position:

    find_focus.py -s "100,10,1" -o "3,8,25" -s 1800 -m 3200

This will run three iterations of the search process. The first one with a step size of 100 and an overshoot of 3 steps, the second one with a step size of 10 and an overshoot of 8 steps, and the third one with a step size of 1 and an overshoot of 25 steps.

Script auto_align.py

Script to perform an automatic camera alignment (tilt & center).

For more information, display the script’s help text

auto_align.py -h

Examples:

  • Perform a completely automatic alignment:

    auto_align.py

  • Perform the alignment to a specified minimum accuracy (0.8 pixels for the rotation and 1.0 pixels for the centering):

    auto_align.py -r 0.8 -c 1.0

  • Limit the maximum number of iterations to 8:

    auto_align.py -i 8