Leginon

h1. Ways of Moving to Targets in Nodes that acquire images inside MSI

Nodes that acquire images at each of the multi-scale mostly belong to a base class called Acquisition and have an icon that looks like a camera. There are many settings related to this main building block with many options for moving the received target to the detector center (targeting, in short).

Targets can be moved to the center of the detector for image acquisition using one of the

following calibrations:

* [[Image Shift matrix calibration|Image Shift]]

* [[Stage Position matrix calibration|Stage Position]]

* [[Modeled Stage Position calibration|Modeled Stage Position]]

* [[Image Beam Shift matrix calibration|Image Beam Shift]]

There are two movers to chose from: Presets Manager and Navigation. Presets Manager provides

a simple one trial movement. It assumes that the move calibration is good enough to reach the

target directly. Navigation Node is more flexible, since it can be configured to perform

multiple trials. However, most of multiple movement benefit is only relevant in the case of

Stage Position/Modeled Stage Position move type. It is also not recommended to be used to

acquire images that queued targets will be selected on.

To achieve a movement of defined tolerance, movement by Navigation Node with multiple

trials checks the error of targeting after each trial move. If the error is larger than the

tolerance, the target location is recalculated from the current location, and the targeting

movement repeated. It was noticed that on FEI microscope, the movement error is lower if the

required move is smaller. Therefore this algorithm allows even a badly performed goniometer to

target accurately, at the expanse of multiple exposure in the general area. At low

magnification and highly binned short exposure, this is usually not a problem.

The settings in the Acquisition Class that determines the above tolerance is named

"Navigator Target Tolerance". You can set this setting to 0 which will turn off multiple move

option and perform the move as if it is Presets Manager.

Occasionally, the additional trials do not further reduce the targeting error due to

sluggishness of the goniometer movement. The user may want either to accept this closest

targeting or to abandon the acquisition sequence. The decision often lies in how long the

acquisition sequence is and how likely that such image with lower standard is likely to be

useful. For example, as a target for tomography tilt series, a missed target can translate to

30 min of wasted scope time. However, a slight miss that causes the target not centered but

still in the view is worth data collection effort.

The settings in the Acquisition Class that determines the above abort/proceed tolerance is

named "Navigator Acceptable Tolerance". The "Acceptable Tolerance" should always be larger

than the "Target Tolerance".

In addition, a final image shift can be applied to resulting multiple move location

although in most cases this does not improves the targeting if the targeting error is already

smaller than 1e-7 m.

______

[[Multi-Scale Imaging Concept|< Multi-Scale Imaging Concept]] | [[Flavors of MSI applications|Flavors of MSI applications >]]

______