This dialog allows you to display isosurfaces of the input volume or a subvolume of it. An isosurface is a surface generated at places where the intensity values cross a threshold value set by the user. The subvolume is specified by a bounding box whose position and size are set by sliders. Isosurfaces are displayed when this dialog is opened but will be removed when you close the dialog.
The isosurface mesh and the bounding box are store in two "extra objects". Their display properties can be edited in the Model View Object Edit dialog. The extra objects that can be edited are listed after the last regular object in the model; just use the slider or spin box there to get to them.
If you click on a position in the isosurface with the right mouse button, that position becomes the current point within 3dmod, thus allowing you to find corresponding features in the image data.
The computations can be done with multiple threads running in parallel. Doing so incurs some extra overhead and the computation time also does not reduce proportional to the number of processors used and may even increase with more than 4 threads on an 8-core system. Thus, the multiple threads are used only if the environment variable IMOD_PROCESSORS is set to a number, and the maximum number of threads used is 4. You can experiment with your system by setting IMOD_PROCESSORS to various values and starting 3dmod with the -DU option.
The isosurface display is based on contouring and surface smoothing modules from Chimera, developed at the Resource for Biocomputing, Visualization, and Informatics at UCSF.
The controls in this window are as follows:
View isosurfaces selects whether the isosurfaces will be computed and displayed.
View user model selects whether the regular model is displayed as well.
View bounding box selects whether a bounding box around the data will be displayed. When it is being displayed, it will also show up in the Zap window regardless of what section is being displayed.
Keep box centered controls whether the dialog will center the subvolume being rendered in the model view window whenever its size or position changes. The subvolume is also centered when this box is turned on, so you can use it to center the volume even if you do not want to leave it on.
Binning selects the amount of binning of the data in 3D; e.g., with a binning of 2, each voxel used for computing the isosurface will be the average of 8 adjacent voxels. Binning will both increase the speed of the display and smooth the surface considerably.
Smoothing selects the number of iterations of a smoothing routine that moves each vertex of the isosurface toward the average of neighboring vertices. Some of the change in appearance when you turn on smoothing may reflect a change in the way the normals to the surface are computed. These normals control how light reflects from the surface. With no smoothing, they are computed from the image data by the Chimera code, but with smoothing, they are recomputed from the triangles in the usual way for IMOD meshes. Note that another way to get a smoother display is to restart 3dmod with the image loaded binned.
Delete small pieces can be turned on to eliminate small pieces not connected to the rest of the surface. The threshold size for eliminating pieces can be adjusted with the Min size spin box, which sets the minimum number of triangles required in order to retain a piece. There is significant computation involved in identifying the small pieces, so you may need to turn this option off while adjusting other features, then turn it back on.
Below these controls is the histogram of voxel values inside the bounding box. The histogram is based on the byte values stored in program memory, not the values in the image file.
Threshold sets the constant intensity value at which the isosurfaces will be rendered.
Link to global X, Y, Z controls whether the coordinates selected in the sliders below will be linked to the current point coordinate in 3dmod image display windows. If it is on, then changing these sliders will change the current point in 3dmod and affect other displays; also, any change in current point within 3dmod will change the center position of the bounding box. If it is off, then the coordinates selected here become independent of the current point. Turning the option off allows you to right-click on the isosurface without having the isosurface display move to a new position.
The X, Y, and Z sliders will track the current point coordinate in 3dmod image display windows and can be used to adjust the center position of the bounding box. The bounding box will center on the coordinate unless that would result in the box size being smaller than the slider value.
The X size, Y size, and Z size sliders can be used to set the X, Y, and Z size of the bounding box. The maximum values of these sliders are set so as to prevent you from trying to render too large a total volume, which is especially time-consuming when the threshold is near the middle of the intensity distribution.
The Use Rubber Band button can be used to set the size and center of the bounding box in X and Y from the position of the rubber band in the top Zap window. The size will be limited to the maximum size allowed for this display but the center position will be the same as that of the rubber band.
Save is used to create two new objects containing copies of the isosurfaces and the bounding box. Until you do this, these items are kept in "extra objects" that are not saved with the model. This button is the only way to save the isosurfaces in a model file and reload them. When the bounding box is saved, it will stop being displayed on all sections in the Zap window. After you save the objects, the model view window will show both the isosurfaces in the extra object and the saved objects, unless you turn one or the other off.