Leginon

h1. Tomography

The Tomography node is a subclass of <link linkend="acq_node">Acquisition</link>. This

node receives a Published Target List and navigates to each target using the specified Move

Type. Then, a series of images at assigned tilt angleis are acquired and published to the

database. Many of the Algorithms are based on UCSF Tomo. The node can also initiate dose

measurement and alignment of zero loss peak for Gatan energy filter.

Be awared that this node multiply the CCD counts by 10 and convert the values into signed

Int16 before it is displayed and saved as MRC file to reduce the file size. Therefore a CCD

counts (after binning and flat-field correction) of 3276.8 or higher will overflow.

<highlights>

Required bindings

<simplelist type="vert">

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

<member> PresetsManagerNode - (PresetChangedEvent) -> TomographyNodeAlias</member>

</simplelist>

</highlights>

<highlights>

Bindings with the previous target makers or click target finder

<simplelist type="vert">

<member> TargetMakerNodeAlias - (ImageTargetListPublishEvent) ->

TomographyNodeAlias</member>

<member> TomographyNodeAlias - (TargetListDoneEvent) -> TargetMakerNodeAlias</member>

</simplelist>

</highlights>

<highlights>

Optional Bindings with DriftManager to allow target correction after drift.

<simplelist type="vert">

<member> TomographyNodeAlias - (NeedTargetShiftEvent) -> DriftManagerNodeAlias</member>

<member> DriftManagerNodeAlias - (AcquisitionImageDriftPublishEvent) ->

TomographyNodeAlias</member>

</simplelist>

</highlights>

<highlights>

Optional Bindings with another Acqusition subclass (for example, Focuser or Acquisition)

that processes target types rejected by Tomography node.

<simplelist type="vert">

<member> TomographyNodeAlias - (ImageTargetListPublishEvent) ->

AnotherAcquisitionSubNodeAlias</member>

<member> AnotherAcquisitionSubNodeAlias - (TargetListDoneEvent) ->

TomographyNodeAlias</member>

</simplelist>

</highlights>

<highlights>

Optional Bindings to Reference subclass (for example, DoseMeasurement or AlighZLP) that

initiates a set process at the reference target position.

<simplelist type="vert">

<member> TomographyNodeAlias - (DoseMeasurementPublishEvent) ->

MeasureDoseNodeAlias</member>

<member> TomographyNodeAlias - (AlignZeroLossPeakPublishEvent) ->

AlighZeroLossPeakAlias</member>

</simplelist>

</highlights>

h2. Tomography Toolbar ( Leginon/Tomography/Toolbar> )

*  same tools are available as for any Acquisition sub Class node.

h2.  Tomography Settings ( Leginon/Tomography/Settings>

)

The top portion is identical to Acquisition/Settings in an Acquisition node. Only the

part related to Tomography is described.

*  Tilt min, max, start, and step angles (in degree).

Start at 0 degree and using a negative step cause the node to collect data in the

negative angles first.

*  Use equally sloped (symmetric) angles, power of 2 angles in 180 degree range can be

used instead of the default equal angle increment.

*  Exposure Total dose is divided by the number of tilt angles to obtain the actual

exposure time with known dose of the preset. The actual exposure time should also be

limited by Min/Max specified.

*  "Before Collection Measure Dose" will acquire a dose image (512x512 at the center

using current preset and at the reference image. The result will update the preset dose

for the data collection dose fractionation calculation.

*  Before Collection Run buffer cycle |Align zero loss peak dose what it says.