The stand-alone application Tracer and the automodel option in 3DModel's options menu will both trace the axis of tubular structures. The tracing done by Tracer is fully automatic. It searches for a point whose intensity is larger than the upper threshold, traces from there, and, after marking the regions already searched, repeats the process. With 3DModel's automodel option, the starting point is an object which contains a single point (unless you use the "monitor steps" option, where the current point of the current object is used). Both assume that the input image data is 16-bit signed integers (shorts) and that it comes from an image window. CopyRegion can be used to force that data to have that form; if you want to scale the data, Image Arithmetic may be used.
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
3DModel | Copy Region | Image Arithmetic | Priism
When run as a stand-alone application, use this field to supply the name of the file to store the traced structures.
For the automodel option in 3DModel, enter which of image windows to use in the "In window" field. For the stand-alone tracing program, the input can come from an image window; the number is specified in the "In" field in the stand-alone program's main dialog.
The stand-alone Tracer, a seed point to start tracing must first be found. Only those points whose intensities are greater than the value shown in the "upper threshold" field are considered as possible seed points (a seed point must also be two or more pixels from the edge of the data set).
The value in the "lower threshold" field is the lowest intensity level that should be considered part of an object.
The points in the traced structure will be a fixed distance, d apart where d is the value shown in the "sample size" field times the x pixel spacing. The step size may also influence the region over which intensity values are averaged; see the search method topic for details.
A recommended value for the step size is one that is greater than half the thickness of the object and less than the distance between separate structures.
When tracing a structure, the program samples the average intensity of blocks of pixels. The size of the blocks is controlled by the value shown in the "sample size" field (for more details also see the description under the search method topic). A good choice for the sampling size is the thickness of the structure to be traced.
In the stand-alone Tracer, the value shown in the "z box" field sets the half-width in sections of the region searched to find a starting point for tracing once a point above the upper threshold is found. Also, once an object is traced, the region about it is marked as already searched. The "z box" value is the half-width in z about the object's axis for the region so marked.
In the stand-alone Tracer and in 3DModel's automodel option when only one point is available to start with, the "z box" field also sets the half- width in z to search when locating the second point in the object.
When considering the next point to be added, a limit is applied to how much the structure can bend. This helps avoid the search from turning back on itself. The maximum deviation allowed from the line joining the two previous points is shown in the menu next to the "max turn" label. The values are in degrees.
When the "gaus" 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.
Two different algorithms are available for tracing structures. Depending on which you use, you may wish to set the step size and sample size differently. Both methods first look straight ahead in the direction of the last two points added to the structure and then in consecutively larger circles around the direction until a maximum integrated intensity is found. The difference in the two algorithms is the shape of the area used to calculate the integrated intensity:
With 3DModel's automodel option, you can choose to have the search algorithm run to completion (it searches until it reaches the edge of the data set or can no longer find any points meeting the intensity threshold; it then returns to the starting point and searches in the opposite direction) or to have the search stop after a certain number of points have been added (subsequent iterations then start at the current point of the current object). To use the former, select the "entire object" option in the "find" menu. For the latter, select the "monitor steps" option in the find menu and enter the number of points to be added in each step into the step limit field.
When using 3DModel's automodel option with the "monitor steps" search method, the value shown in the "step limit" field is the maximum number of points that will be added during each search. If the limit is zero, the search will continue until a boundary set by the lower lower threshold is crossed (i.e. just as if the "entire object" search method were used).
When run from 3D Model, press the "Start search" 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 the "undolast" button will undo the points added to the model by the last search. If the "entire object" option is used, this will also undo your starting point, so you will need to reselect a new starting location.