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Command: bumps

bumps  volume-model  center  center-spec  [ range  r ] [ baseArea  a ] [ height  h ]  other-options

bumps  reportbumps-markers ] [ save  filename ] [ signalMap  volume-model ]

The bumps command identifies and marks isosurface protrusions. It was developed to analyze cell-surface protrusions in volume data from light microscopy. Surface distance maxima from a central point are identified in the highest-level contour surface of the specified volume model, and markers are placed on these maxima. The center is typically a single marker that was added previously with the mouse using the place marker mode set to mark the center of the surface (see Marker Placement). A single atom could also be used. See also: volume, Volume Viewer


bumps #1 center #2 height 1 base 100 range 75
bumps report #3 save ~/Desktop/prot.txt signalMap #4

Conceptually, rays are followed out from the center up to the range distance, and distance maxima in the isosurface are identified. The rays for maxima are followed back toward the center until the cross-sectional area of a candidate protrusion reaches the base area value. Candidate protrusions are then compared to the height criterion. If multiple maxima share a single base, the highest one wins. This algorithm finds protrusions that are radially oriented with respect to the center, and is likely to miss ones that are significantly bent or that point in different directions.

The bumps report command reports statistics for previously identified bumps (isosurface protrusions). One or more marker models previously created with bumps can be specified; otherwise, all of them will be included. The information is shown in the Log unless the save option is used to save it to a file instead, where filename is an output file pathname or the word browse to specify name/location interactively in a file browser window. For each identified bump, the information includes:

If a signal map is specified, the sum of its values over grid points within the protrusion is also reported.


range  r
How far out from the center to look for protrusions in the physical distance units of the data, typically μm (no default; if no value is given, the full extent of the data is examined).
baseArea  a
The cross-sectional area defining the base of a protrusion (default 10.0) in physical units of area (typically μm2).
height  h
The minimum height of the surface peak above the base to identify a protrusion (default 1.0), in physical units of distance.
markerRadius  radius
Size of the markers added to mark protrusions (default 1.0).
markerColor  color-spec
Color of the markers added to mark protrusions identified by the algorithm (default
). The allExtrema option can be used to mark all maxima, even those not meeting the algorithmic criteria, using additional colors.
name  model-name
Name for the added marker model (default bumps). See also: rename
colorSurface  true | false
Whether to color the identified protrusions (default true). The coloring is random and intended mainly to delineate the protrusions from the rest of the surface. It applies to surface points within one voxel of the grid points associated with the protrusion.
allExtrema  true | false
Whether to add markers for all distance maxima, including those otherwise omitted by the algorithm (default false). Markers for maxima that would have been excluded are color-coded: Markers for maxima meeting the algorithmic criteria are colored according to the markerColor option (default

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2017