Tracer / Automodel is a (semi-)automatic searching tool for tracing the axis of a tubular structure. Tracer is a stand-alone application which starts tracing the structures from pixels whose values are larger than the upper threshold. Automodel is available from 3D Model's options menu; it starts from the current object which must contain only a single point (unless you use the monitor steps option) which serves as the starting point. Automodel allows you to monitor the progress of the search as it progresses. Both assume that the input data is in a 2 byte integer (short) format; if it is not, use Copy Region to scale and convert it to that format.
Overview | Model file | Window | Upper threshold | Lower threshold | Step size | Sample size | Z box | Max turn | Gaussian | Search method | Find | Step limit | Start search | Undo last
Priism | 3D Model | Copy Region
When run as a stand-alone application, use this field to supply the name of the file to store the traced structures.
When run from 3D Model, use this field to enter the number of the window whose data will be used for tracing.
Pixels with values greater than this threshold are used as starting points for the traced structures when Tracer / Automodel is run in stand-alone mode.
Pixels with values lower than the lower threshold are considered to be outside of the structure to be traced. The search for new points in a structure terminates if no points can be found which are greater than the lower threshold.
The step size specifies the distance, in pixels, between adjacent points in the model. The step size should be at least half the thickness of the structure to be traced and less than the distance between separate structures.
While searching for the next point in the structure, the intensity is averaged over a box-shaped region (when the Gaussian option is on this is a weighted average). The dimensions of the region are sample size pixels in each direction. A good choice for the sample size is roughly the thickness of the structure to be traced.
When used in the stand-alone mode (fully automatic search), the Z box is the number of adjacent sections which are searched to determine the second point in a structure after the first point has been determined from the upper threshold criterion. The Z box is also used in the stand-alone mode to specify the region that is zeroed about the structures that have been traced so far.
This field defines how sharp of an angle you are willing to let the object turn from one point to the next. This parameter helps avoid the search from turning back on itself and going down the same structure in the opposite direction, and possibly prevent the search from turning off onto some brighter structure.
When this toggle is on, the intensities averaged over the sample region are weighted so that the those close to the center of the region contribute more than those on the edge.
There are two search methods that you can use. Based on the method you may want to set sample size and step size differently. Both methods first look straight ahead in the direction of the last two points then in consecutively larger circles around that direction until a maximum integrated intensity is found. The difference in the two methods is in the shape of the area where integrated intensity is taken:
When run from 3D Model, you have the option of setting how often to intervene in the process of tracing the structure. With the entire object option an object is traced in both directions until the edge of the structure or dataset is found. With the monitor steps option, the structure is only traced for up to the number of points set in the step limit field; when it stops you can continue the search by pressing the Start Search button or manually select additional points.
The step limit sets the maximum number of points that will be added to the current structure when the monitor steps option is selected. If the limit is zero, the search will continue until a boundary set by the lower threshold is crossed.
When run from 3D Model, use this button (or the s key while the mouse is positioned over the window used for tracing), to start tracing a structure or to continue tracing a structure when using the monitor steps option.
When used from 3D model, pressing this button will undo the points added to the model by the last search. When using the entire object option, this will also undo your starting point, so you will need to reselect a new starting location.