Good Alignments Save Time¶

Leginon relies on a stable microscope. The most likely reason for leginon to fail performing is bad microscopy alignment. Various bad alignments often compound the difficulty in problem solving. The requirement of leginon for good alignment is higher than most users who set up low dose image acquisition directly at the scope are used to, especially regarding alignment in LM mode since most low dose user has limited usage for LM mode images.

Apart from alignments that every user does without Leginon, Here are some of alignment critical to Leginon MSI applications but not a common low-dose kit users.

HM beam-tilt pivot point and current rotation center set for eucentric focus¶

These are needed for beam-tilt based auto-focusing

Defocus reset to eucentric at BOTH HM and LM modes¶

These are important starting point to allow consistent performance of calibrations and saved presets.
If your scope control panel has a "go to eucentric focus" button, and the set point is no more than 3 um off in HM and 10-20 um off in LM, it would be good enough to just press that and then reset defocus.

What is eucentric focus?

Image/Beam Calibration at HM mode¶

Beam has to remain centered at CCD camera when Leginon move to targets with image shift. For FEI scopes, the calibration procedure is in Tecnai/TEM User Interface. For JEOL scopes, a calibration is performed in Leginon to achieve the same effect.

< Calibrations required on FEI microscopes | Microscope Set-up Checklist >