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 stored 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 isosurfacing is always computed on a subvolume of byte values, even if data have been loaded into the program as 16-bit integers instead of bytes. In the latter case, the scaling to bytes is determined by the the Low and High sliders in the Information window. In order to have good dynamic range in the intensity values being analyzed, be sure that the Low and High sliders are set so that images have a good contrast with a fairly wide range between the Black and White sliders. Using the autocontrast function generally leaves the sliders in positions that will allow good scaling for display. Changing the Low and High sliders will change the effect of the threshold setting here.

If you have multiple volumes loaded, separate thresholds are maintained for each volume, so when you return to a volume, it will be shown at its own threshold. When you first step to a volume that has not had its threshold set yet, it will be given a threshold at the same percentile point in its intensity histogram as for the previously displayed volume.

The computations will be done with multiple threads running in parallel if the system has multiple processors. 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 maximum number of threads used is 4, regardless of how many processors are available. Up to 4, the number of threads is set by the apparent number of processors on the system, or by the value of the environment variable IMOD_PROCESSORS if it is set. If your machine has hyperthreading enabled, the program will probably run better if you avoid using hyperthreads by setting IMOD_PROCESSORS to the actual number of cores on the system. You can experiment with your system by setting IMOD_PROCESSORS to various values and starting 3dmod with the -DU option in order to see some time outputs. Display a large portion of a volume so that processing takes hundreds of milliseconds.

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 in two columns. The left side has controls for setting the threshold and adjusting the volume being displayed; the right side presents a variety of options. Controls are as follows:

At the top left 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.

The Threshold slider sets the constant intensity value at which the isosurfaces will be rendered. When you open this dialog, the threshold is automatically set to a certain percentile on the low side of the intensity distribution so as to show dark structures. There is an option in the Look/Limits tab of the 3dmod Preferences dialog to have the initial threshold set on the high side so as to show light structures instead. Also, you can use the hot key F11 to switch the threshold to an equivalent point on the other side of the median.<

The Outer limit slider sets a second threshold beyond which intensity values will be set to the median intensity, so that you can visualize just the intensities between two values. However, extreme intensities are usually surrounded by less extreme ones; thus, if the program removed only the extreme ones from consideration, you would usually see a shell around places with extreme intensities. To avoid this effect, the program searches up to 16 pixels away from extreme pixels for ones that are above the threshold and sets those to the median as well, as long as they are connected to an extreme one by a chain of adjacent pixels above the threshold. The outer limit is constrained to be on the same side of the median intensity as the threshold. No elimination is done when the outer limit is at the end of the intensity range.

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 maximum number of voxels allowed, as well as the number of voxels when the display first opens, can be controlled in the Appearance tab of the 3dmod Preferences dialog. The spin boxes there set the size of a cube equivalent to whatever shape of volume is displayed. Thus, display time will increase with the cube of these numbers.

The Rubberband 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 or Slicer window with a rubber band. For a Slicer window, the position of the rubber band in the viewing plane is transformed to coordinates in the volume to obtain the minimum and maximum X and Y coordinates to assign to the bounding box. 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.

The Contour button in the "Set X/Y area from" box allows you to set the size and center of the bounding box to fit the current contour when you are masking the volume with the current contour (see below). When masking with the lasso in a Zap window, the button (now labeled Lasso) will fit the bounding box to the lasso. When masking with the current object, the button (now labeled Object) will set the X/Y area based on the extent of the current object over the selected Z range. This button is useful for recentering if you change the current contour or object or the center or size in Z.

Painting the Mesh: It is possible to set different parts of the isosurface to different colors or transparencies by enclosing them in the spheres of a scattered point object. To activate painting, turn on the Paint obj. check box and enter the object numbers of one or more scattered point objects in the text box (a list with comma-separated ranges is allowed). You will need to define an object as scattered point type before entering it, or its number will be removed from the list.

• There are two ways to have more than one color. The easiest way is probably to have separate objects. However, originally, all spheres had to be in one object, and it was necessary to use the Fine Grain dialog. If for some reason you still use this mechanism, it is probably easiest to keep track of different colors by assigning colors to individual contours instead of points. Select the Contour radio button at the top of the dialog and use the Set button in the "Line color" section to set the color of the current contour.
• You can adjust sphere radius for individual points with the Surface/Contour/Point dialog, with the mouse scroll wheel in the Zap window if Set with mouse wheel is checked in that dialog, or directly in the Model view window with the scroll wheel and Ctrl and Shift keys held down.
• Spheres can overlap. Use overlapping spheres of the same color to paint a non-spherical volume. When two spheres of the different colors overlap, there will be a sharp boundary between the two colors. If one sphere is contained entirely within another, then parts of the mesh inside the smaller sphere will be that sphere's color, and parts outside that sphere will be the larger sphere's color. Thus, you can make concentric shells of different colors.
• If the painting object is the current object, you can hold down Ctrl and Shift keys and do several modeling operations directly in the Model View window, aside from adjusting the size of the current point with the scroll wheel. You can move the mouse with the left button held down to shift the current point in the X/Y plane of view. Arrow keys and the PageUp and PageDown keys (not on the numeric keypad) can be used to shift in X/Y and in Z as well. Click the middle button to insert a new point in the current contour. Use the Delete key to delete the current point. Click the right button to select a different scattered point; a point on the isosurface will not be picked as long as Ctrl and Shift are held down. There are hot keys to move to the next or previous object, contour or point, listed in the "Model Editing Operations" section of Model View Keyboard Commands. Some are described in terms of taking just the Ctrl key, but on a US keyboard all of them will work with Ctrl and Shift held down except for Ctrl+Shift+0 (i.e., Ctrl-), which is an alternative to Ctrl-} ).
• The "Subsets" panel of the Edit Objects dialog has an option to display only the current point; this may be useful for focusing on just one point at a time when working on the painting object.
• Transparency can also be applied with a painting object, although there may be limitations. To erase a part of the mesh, the best way is to set transparency to 100 in the Edit Objects dialog for the object as a whole, or in the Fine Grain dialog for individual contours or points. Rendering will be slower with transparency. Artifacts often appear when two partially transparent items are superimposed.

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.

Link to global X, Y, Z controls whether the coordinates selected in the sliders on the left 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. It is also useful when modeling scattered points directly in the Model View window in order to paint the isosurface (see below). Finally, if the button is off, a masked isosurface will change dynamically as the masking contour, object, or lasso or modified in a Zap window.

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.

Filter sigma selects a sigma value for filtering the image data in 3D with a Gaussian kernel. This filter is applied after binning, if any, and the sigma is in binned pixels. Sigma can range from 0.5 to 3.0, with the kernel going from 3x3x3 at sigmaup to 1.0, to 5x5x5 at sigma up to 2.0, and 7x7x7 above that. This filtering can produce a smoother surface than binning alone, but it can be time-consuming with larger kernel values and a large volume to filter. The best approach for a smoother surface and fewer disconnected pieces would be to bin less than is needed, then try filtering with sigmas around 1 - 1.5.

Smooth mesh 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 binning and kernel filtering will are both ways of smoothing that reduce extraneous pieces and protusions due to noise, while this method is less effective for that purpose.

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.

Cap at box faces can be turned on to close off isosurfaces that go to the edge of the bounding box. Otherwise, you will see into the inside of any isosurface that is cut by the bounding box.

Masking: It is possible to restrict the region within the bounding box that is rendered with one of the selections in the Mask box.

• Select Current contour to see isosurfaces just inside the current contour, provided the current object is closed type. The same area will be shown for all planes in Z being displayed. When you first select the option, the bounding box size and center will be adjusted to just fit the contour if possible; if the contour is too large, the size will be restricted but the center will be set the same. However, the subvolume will not be continually refit if you change contours or modify the current contour, unless the Link to global X, Y, Z button is turned off. Press the Contour button in the "Set X/Y area" box to refit to a new or modified contour.
• Select Current object to see isosurfaces inside of contours of the current object, provided it is closed type. The Z size and center sliders control the range of data that will be displayed in Z. You need not have a contour on each section in the range; the program can smoothly interpolate between the contours that you have drawn. Specifically, for a section that has no contours, the program finds the nearest sections above and below in Z that have contours. If there is only one contour on each section, an interpolated contour is computed by forming a mesh between the two given contours and is used to constrain the isosurface on that section. However, the interpolation is not possible if there is more than one contour on one of the sections, in which case it just uses the contour(s) on the nearest section. Other than this limitation, there is no problem with having more than one contour on a section. Just as described for Current contour, the bounding box will be set in X and Y to fit the object when the option is first selected, but if you change the current object, you need to push the Object button to refit the subvolume.
• Select Sphere to see isosurfaces within the largest sphere that fits inside the bounding box. The sphere will be centered on the position indicated by the X, Y, and Z sliders, unless the sphere would be truncated at that position. Thus, if you make the bounding box large enough so that it does not change when you move one of these sliders, you can move the sphere around within a fixed subvolume.
• Select Ellipsoid to see isosurfaces within an ellipsoid that touches all the faces of the bounding box. Use the X, Y, Z size sliders to adjust the shape of the ellipsoid.
• Select Zap lasso to see isosurfaces just inside the lasso in the top Zap window that has a lasso drawn. This works the same as when Current contour is selected, except in one respect. There are two ways of shifting the lasso in a Zap window: directly with the first or second mouse button when it is within 10 pixels of the lasso contour; or using the contour shifting/transforming enabled with the Shift+P hot key when no current contour is selected. With the first way, the isosurface is updated only when the lasso movement is stopped (provided that Link to global X, Y, Z is turned off). With the second way, the isosurface is updated as the lasso is shifted or transformed, just as when masking with the current contour.

Save Object 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 and the next one are 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. If you have painted the isosurfaces, the current painting is stored as part of the new object and cannot be modified.

Sort & Save is used to sort the triangles in the isosurfaces into different mesh components for each physically separate piece. These meshes are given different surface numbers and stored in one new object (the bounding box is stored in another object as well). Once a mesh with surface numbers has been saved, the following capabilities are available for working with such objects:

• Whenever the current object contains only meshes and they have surface numbers, the program maintains a current surface number for mesh-only objects. Right clicking on the display of the object will set this current mesh surface number.
• The Surface/Contour/Point dialog both shows what surface is selected and allows you to change the current surface. For example, you could choose Surface only in the "Subsets" panel of the Edit Objects dialog then step though the surfaces to see one at a time.
• The Fine Grain dialog allows you to modify the properties of the current mesh surface once you have selected Surface at the top. The four items meaningful in the 3D display can be modified: line color, fill color, transparency, and 3D line width. This dialog keeps track of the last change applied, and the hot key "Ctrl-F" in Model View will make it apply that change to the current selection, if the Last button for the particular change is still enabled. Thus, you can easily color multiple surfaces by repeatedly right clicking on a surface to select it and then typing "Ctrl-F". If part of the mesh was painted before saving, the painting will be retained because it consists of fine grained changes inside the mesh that override changes at the surface level.

  Information Stored in the Model Several settings are stored in the model structure and also in the model file when it is saved: the outer limit, binning, sigma for kernel filtering, smoothing iterations, whether small pieces are deleted and the minimum box size, and whether to cap at the faces of the box. Only one value of these settings is saved, but the threshold is saved by time index if multiple image files are loaded. The threshold is stored by its corresponding value in the image file, so that is it possible to reopen 3dmod with different scaling of the data and achieve a similar effective threshold. The paint objects are also flagged as such in the model, so the list of paint objects will be restored when reopening 3dmod or the isosurface display. With all these items being stored, it should be possible to reopen an image file being painted and have the display restored to its previous state.

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