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Tomography


  1. Place sample on the stage
  2. Position the sample in the field of view of the microscope. Use the top view camera as an aid.
  3. Check the alignment of the centre of rotation between 0 - 180 degrees and 90 - 270 degrees. Do the coarse alignment using the goniometer head and the fine alignment with sampx and sampy.
  4. When using the Maia detector:
    1. Once aligned and using the Maia detector, move the Maia partially in place to check the space between sample mount and Maia over the full rotational scan range.
    2. Move the Maia in measurement position
  5. Perform a tomography alignment scan
    1. Set the tomography scan mode to incremental:

      scanmode_use tomography_mode 0
    2. Create a new session:

      Example
      newsession <sample_name>_tomo_alignment
    3. Perform a tomography scan:

      Example
      ctomomesh samy 1 2 100 samz 1 2 100 samr 0 270 10 0.0005
    4. Open the scans and check the alignment and select the scan range
    5. Iterate if needed.
  6. Start the tomography scan:
    1. Start a new session
    2. Set the tomography scan mode to the desired mode, see HERE.

      Example for golden angle
      scanmode_use tomography_mode 1
    3. Start the scan:

      Example
      ctomomesh samy 1.1 1.9 400 samz 1.2 2.1 450 samr 0 360 180 0.001
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