AutoModel Options

Use

To...

Window

Enter the window to use for the search.

Lower Threshold

Specify the lowest intensity that should be considered part of the structure. This defines the end of the structure.

Step Size

Specify how far apart in X (pixels) each point of the model should be. A good step size is at least greater than half the thickness of the object.

Sample Size

Specify the diameter for a block of pixels. To trace the structure, the program samples the integrated intensity of a block of pixels with this diameter. A good sampling size is the thickness of the structure.

Z Box

Find the depth in Z to zero by zeroing through data already found. If the search is started after only one point is selected, Z Box will be used to decide how far in Z to look for the highest intensity when looking for a starting search direction.

Max Turn

Define how sharp of an angle you are willing to let the object turn from one point to the next. This parameter helps to prevent the search from turning back on itself and going down the same structure in the opposite direction. It also prevents the search from turning off onto some brighter structure.

Gaussian

Specify whether or not to weight the center of the sampling area higher than the outer part.

Search Method

Choose which of two search methods to use. Depending on which method you choose, you may want to set sample size and step size differently. Both methods search first 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.

Max Intensity uses a sphere centered at each test point with a radius of Sample Size/2.

Max Tube uses a cylinder of length Step Size and of radius Sample Size/2.

Find

Specify the level of interactivity to use.

Entire Object specifies to keep searching until the edge of the structure or the data set is reached. Then start back at the initial point and search for more structure in the other direction.

Monitor Steps specifies to search for only as many points as you set in the Step Limit. If Step Limit is set to zero, softWoRx searches until it hits the threshold boundary. It continues searching from where it stops if you click Start Search again.

Start Search

Begin searching (you can also use the S-key).

Undo Last

Undo all points in the object or the last set of Step Limit points.

If you are in Entire Object mode, this undoes all the points of the object just found, but leaves that object as the current object so you can try again.

If you are in Monitor Steps mode, only the last set of Step Limit points is undone.