Manpage of seedSpikes
Section: User Commands (1)
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seedSpikes - Create a seed model for identifying particles ("spikes")
on the surface of a sphere or cylinder by template matching.
seedSpikes inputModel outputModel
seedSpikes inputModel outputModel type
seedSpikes inputModel outputModel type delta
seedSpikes inputModel outputModel type delta dR
seedSpikes inputModel outputModel type delta dR maxPos
Given an input model defining a number of spheres or cylinders (see
below for conventions), generate a new model with candidate spikes
distributed over these surfaces. The candidate spikes will be placed dR
voxels outside the surfaces with an approximate spacing of delta. Delta
can be specified either in degrees (if positive) or voxels (if negative).
The output model will be suitable for use with spikeInit to create an
initial motive list followed by semi-automatic particle picking using
PEET's flgNoReferenceRefinement option for matching with a user-supplied
- inputModel = string
The path to the input model. In the spherical case, the input model
must consist of single-point objects with coordinates defining the
centers and point sizes equal to the radii of the spheres. In the
cylindrical case, each object must contain only a single 2-point contour
defining the radius, axis, and extent of the cylinder. For helices, in
addition to the definition of the cylinder in contour 1, each object must
also contain a second contour containing 1 or more start points for the
- outputModel = string
The path to the output model. Spikes corresponding to each sphere or
cylinder will be put into an odd-numbered object, followed by an
even-numbered object containing the (input) description of the shape.
This format is suitable for use with spikeInit.
- type = < 'sphere' | 'cylinder' | 'helix' > (Default = 'sphere').
Specify spherical, cylindrical, or helical processing.
- delta = float (Default = 10 degrees)
Approximate spacing between seeded spike locations. For spheres and
simple cylinders, delta may be specfied either in degrees (if positive)
or voxels (if negative). For helices, delta must contain a pair of
signed numbers representing the angular spacing between neighboring
helix points in degrees and the axial distance between them in voxels.
- dR = float (Default = 0 voxels)
How far outside (if positive) or inside (if negative) the surface the
seeds should be placed.
- naxPos = array of 1 or 3 floats ([xmax, ymax, zmax]; Default = )
If specified, seeds will only be placed within 0..xmax, 0..ymax, and
0..zmax. This can be used to prevent seeding points close to the edges
or completely outside of the corresponding volume. If only 1 number is
specified, it will be applied to all 3 dimensions.
averageAll(1), alignSubset(1), modifyMotiveList(1), PEET(1), spikeInit(1)
- SEE ALSO
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using the manual pages.
Time: 16:44:59 GMT, March 05, 2018