Leginon

h1. Focuser

The Focuser node is reponsible for focusing. Focus sequence determines the sequence of

focus steps that can be applied to the focus target the node recieved. For each item in the

sequence, a preset is chosen for imaging and the method of focus (Autofocus or Manual focus)

is selected. For autofocus method, defocus and astigmation are measured by beam tilt induced

image shift. Alternatively distance from the eucentric height is measured by two opposit stage

alpha tilts. The correction type then determines which and how the correction is made. Manual

focus, either through a z height or defocus change, is possible. Eucentric focus can be send

to/recieved form the scope, and the user can also reset current zero defocus. Note that when

stage z is used for focus correction, drift is declared automatically so that the drift

manager can handle the position change properly.

When the stage is tilted significantly, distortion of the image occurs when beam is

tilted. Cosine stretching (Ziese et al. 2003 J. Microscopy 211,179-185) boosts the correlation

peak during autofocusing. In addition, a defocus offset is made according to the tilt geometry

so that eqiuivalent level of defocus is achieved with image shift at any targeted location.

This correction is made automatically.

<highlights>

Required bindings to Presets Manager

<simplelist type="vert">

<member> FocuserNode - (ChangePresetEvent) -> PresetsManagerNode</member>

<member> PresetManagerNode - (PresetChangedEvent) -> FocuserNode</member>

</simplelist>

</highlights>

<highlights>

Focuser normally recieves rejected target list from acquisition node rather than from a

TargetFinderNode Class although it is possible, too.

<simplelist type="vert">

<member> AcquisitionNodeAlias - (ImageTargetListPublishEvent) -> FocuserNode</member>

<member> FocuserNode - (TargetListDoneEvent) -> AcquisitionNodeAlias</member>

</simplelist>

</highlights>

<highlights>

For the focuser that initiates drift monitoring, two bindings are needed.

<simplelist type="vert">

<member> FocuserNode - (DriftMonitorRequestEvent) -> DriftManagerNode</member>

<member> DriftManagerNode - (DriftMonitorResultEvent) -> FocusNode</member>

</simplelist>

Required Bindings to use drift check image for auto focusing.

<simplelist type="vert">

<member> DriftManagerNode - (AcquisitionImagePublishEvent) -> RCTNode</member>

</simplelist>

</highlights>

<highlights>

Bindings needed if to be Fourier transformed

<simplelist type="vert">

<member> FocuserNode- (AcquisitionImagePublishEvent) ->FFTMakerNode</member>

</simplelist>

Focuser node may need target shift correction upon drift.

<simplelist type="vert">

<member> FocuserNode - (NeedTargetShiftEvent) -> DriftManagerNode</member>

<member> DriftManagerNode-(AcquisitionImageDriftPublishEvent) -> FocuserNode</member>

</simplelist>

</highlights>

<highlights>

Optional Bindings with Navigator to allow (iterative) target move correction.

<simplelist type="vert">

<member> AcquisitionNodeAlias - (MoveToTargetEvent) -> NavigatorNodeAlias</member>

</simplelist>

</highlights>

h2.  Toolbar

*  Settings = set acquisition and ice melting parameters

*  Focus Sequence = set sequence and focus parameters

*  Play|Pause|Abort = Restart|Pause|Abort focus target processing.

*  Simulate Target|LoopPlay|LoopAbort= Single acquisition|Multiple acquisition with

time delay|Stop multiple acquisition of a simulate target

*  Browse Image= Load an image and publish it from this node and pass on for

processing.

*  Manual Focus = open the Manual Focus (continuous image acquisition) display to

manually correct defocus or stage z

*  Align Rotation Center = use the current autofocus calibration to align the

rotation center beam tilt.

h2.  Settings

*  See <link linkend="acq_node">Acquisition node Settings</link>

*  Ice melt time (s) = time the acuisition preset will be fixed over the carbon of

an ice grid in order to melt the ice for a better autofocus result. The main screen is

lowered to protect th CCD during the long exposure.

*  Acquire final image = enabled means the acquisition image will be acquired after

completion of all focus sequence.

h2.  Focus Sequence Settings

*  Sequence = add and select the sequence item to which the settings apply.

*  Enable = perform the focusing function of the selected sequence item.

*  Preset = select the preset used in the focusing.

*  Focuse method = Manual | Beam Tilt | Stage Tilt

*  Autofocus

*  Beam tilt (mrad if Beam Tilt; degree if Stage Tilt)= the amount the tilt

will be when running the autofocus routine

*  Use "phase or cross" correlation to register image shift in the autofocus

*  Fit limit = refers to the fitting residual in the tilt induced image shift

equation that determines the defocus and astigmation. If no stigmator

calibration was done, the limit need to be higher.

*  Correction type = Defocus | None | Stage Z

*  Check for drift greater than "3e-10" meters/s (off by default)

*  Stigmator correct = enabled means that astigmatism will be corrected

*  Stigmator Defocus Min/Max = minimum and maximum defocus values (m) used for

correcting the astigmatism

h2.  Manual Focus

*  Settings:

- Mask radius: "1" % of image = center percentage of FFT that is masked out in

order to see the FFT easier on the screen

- Icrement: 5e-7 m = the incremental amount of defocus or stage z change

*  Play = restart continous image acquisition

*  Pause = pause the continous image acquistion

*  Stop = stop the continuous image acquisition

*  "Defocus | Stage Z" = correction options

*  Plus | Minus = increment by Defocus or Stage Z

*  <blank> m = value that can be set with Set Instrument button

*  Set Instrument = send the above defocus/stage Z value to the microscope

*  Reset Defocus = reset the defocus to zero at the microscope

*  Eucentric from instrument = save eucentric height value from the

microscope

*  Eucentric to instrument = send the saved Leginon eucentric height to the

microscope

*  Image = show the current image

*  Power = show the FFT of the current image

h2.  Align Rotation Center

*  Align the beam tilt to the rotation center based on the current defocus/stigmator

calibration.