The radio buttons at the top are used to select whether properties are being shown and controlled for the current Point, Contour, or Surface. For the current item, the various controls show the existing display properties of that item. For each property, there appears the letter D if the property has a default value, or S if the property has been set.

The fine grain changes operate somewhat differently for points than for contours and surfaces. For points, when a property is set for one point, its value applies to all following points in the contour until the change in property is ended, or until a different value is set for a later point. Thus, when a property has a non-default value for the current point, an End button is enabled to allow you to end the sequence of changes at that point. In addition, a Clear button is enabled, which will allow you to reset that property to the default for the whole contiguous sequence of points that have the property set. There are two exceptions to this pattern: Gap to next point applies only to the single point at which it is set, so that one can create an opening in a contour. The Mesh Connection # also applies only to a single point.

For contours and surfaces, all changes apply only to a single contour or surface, or to a selected group of contours rather than a contiguous set of them. Thus, once a property has been set, the Clear button is enabled to allow you to restore the default value, while the End button has no function.

Once you have set a property, the Last button is enabled so that you can conveniently apply the same change to other items, for example points in a corresponding position on another contour.

If the Change all selected contours checkbox is turned on, then changes will be applied to all currently selected contours. This feature is enabled only when contour properties are being controlled. You can use Ctrl and the first mouse button to select multiple contours in the Zap window, where they will be drawn extra-thick. You can also select multiple contours using Ctrl and the right mouse button in the Model View window (to see the selected contours there, turn on Thicken current contour in the Lines panel of the Edit-Objects dialog). In both cases, moving the mouse while holding down Ctrl and the relevant button will select contours crossed by the mouse. All properties except connection numbers can be changed in tandem for the selected contours.

The Draw dashed lines at gaps checkbox lets you see where you have inserted gaps in contours. This is especially useful for seeing line segments on the ends of open-type contours in closed contour objects. Such segments are added so that the whole contour will not cross itself or any other contours that it is meshed with.

The Draw mesh connections checkbox allows you to visualize the mesh connections that have been defined for individual points (see below). At each point with a mesh connection, a square will be drawn in the Zap window; the size of the square is the assigned mesh connection number plus 4.

The "Go to" Previous and Next "Change" buttons can be used to step backward to the last item or forward to the next item where a change occurs. When point properties are being displayed, this will move the current point to the point where that change occurs (which can be the end of a change or the beginning of a new one). With contour properties displayed, the program will move to the next contour with a nondefault property; and with surface properties displayed, it will move to the first contour of the next surface with changes.

If the rubberband is on in the Zap window and positioned over the current contour, then pressing a Set button will apply the property change to all the points and line segments within the rubberband. This feature should make it easy to change several properties in tandem, and to apply similar changes on successive sections. If any of the included points already has this property set, then those changes will be cleared out first, as if the Clear button were pressed for every point in the range. Unfortunately, this feature will not work on both the start and end of a contour if the rubberband spans the endpoints of the contour.

Most property changes will show up immediately in the image or model view windows. However, properties that affect a mesh display will have an effect only after being incorporated into the mesh, and you will not see any change in the display of the mesh until the model is saved, remeshed with Imodmesh, and reloaded. Changes in surface properties are a potential exception to this rule. Ordinarily, Imodmesh encodes surface information into the mesh just like the lower levels of information. However, surface properties are not encoded in the mesh if the object has multiple meshes with different surface numbers. Instead, they are applied during model display, because in this case each mesh can be identified by surface number. As a result, surface properties can be changed dynamically and visualized immediately. There are three ways to get such meshes: 1) meshing surfaces separately with the -S option to Imodmesh or the Surface option in the "Meshing" panel of the Model View Edit Objects dialog, 2) saving an isosurface object into multiple meshes with surface numbers using the Sort & Save button in the Isosurface dialog, or 3) splitting a single mesh saved from the Isosurface dialog into surfaces with Imodsortsurf. Note that in the latter two cases, the mesh has no corresponding contours, and the only way to select a surface in it is to right-click in the Model View window or to use the Surface/Contour/Point dialog.

A final general note before descriptions of individual properties: the ability to make these fine grained changes in the model represents a big change in the potential content of IMOD models. Many programs outside of 3dmod will ignore, discard, or garble this information until they are modified to handle it properly. Even some operations within 3dmod will not deal with the fine grained data correctly, notably sorting of points and use of the line tracker.

• Line color is the color of lines in image and model views, and the default color for mesh displays in model view. Pressing the Set button opens a standard color selector window. When the color is changed in this window, the changes are applied to the current point or contour, not necessarily to the same item that was selected when the window was opened.
• Fill color is the color used for displaying filled meshes when the Use fill color option is selected in the fill color panel of the model view Object Edit window. For spheres, changes here will show up immediately when either this option or Use for spheres is selected; but for other meshed items, the changes will not show up until incorporated into a mesh. The Set button opens a separate color selector window which works like the Line color window.
• Transparency is a property that appears in the model view. Changes will appear immediately for line or sphere displays but will have to be incorporated into a new mesh for filled mesh displays.
• 2D line width, Symbol type, and Symbol size are properties that appear only in 2d (image) displays and their default values are set in the 3dmod Object Edit window.
• 3D line width governs the width of lines displayed in the model view.
• Gap to next point introduces an opening in the contour after the current point, so that contours can have multiple openings. These gaps are introduced into the mesh when the model is meshed with Imodmesh or in the Edit-Objects dialog of the Model View window. The hot key for toggling this property is Ctrl+G and it is available even when the dialog is closed. When contour or surface properties are being shown, this button mutates to Turn off drawing, which lets you turn off an individual contour or surface.
• No mesh cap can be set for a contour to indicate that no cap should be added to it when meshing. This applies to closed contours as well as to the tube and dome caps that can be put on the ends of open contours meshed as tubes.
• Mesh connection # also has several different meanings.
  1. When point properties are being shown, it can be used to force particular points in contours on adjacent planes to be connected in a mesh and to prevent some connections. The meshing routines attempt to match up gaps that are close to each other in two contours being meshed together, and then connect their starting points together and their ending points together. If this process fails, you may have to specify which points to connect with connection numbers. The points to be connected need to be assigned the same unique connection number (unique within the pair of contours being connected). It may be necessary to connect three points rather than two to guarantee that a gap connects correctly between contours. If there are more than three points with the same connection number, points after the third one will be silently ignored when meshing.
     There are two cases where connections can be prevented:
     • At the ends of two contours in an open contour object, or two open contours in a closed contour object. Here, the same connection number should be assigned to the end of one of the contours and to an interior point of the other contour where you want the mesh to end (the two points marked "1" in the diagram below, where "X" is the end of the lower contour). Then assign a unique connection number to the next point out from that interior point (the point marked "2", which is adjacent to "1" in the lower contour).
       

                   1----------...
          X------2-1----------...
       

     • Between two sets of connected points when meshing two contours in a closed contour object. Typically this would be a place where you define a gap in one of the contours, or it would be the place where the open end of an open contour connects to a closed contour. In the diagram below, the upper contour has either a gap or an open end between points marked "1" and "2". The desired points for them to connect to in the lower contour are marked "1" and "2" there. If the points just adjacent to them are marked with a unique value ("3"), then no mesh will be made between the line connecting points "1" and the line connecting points "2". These points block the mesh from filling up the gap on the lower contour.
       

            ...-----1                  2------...
            ...------1-3-----------3-2--------...
       

  2. When point properties are shown, connection numbers can also be assigned to adjacent contours on the same plane to control where a bridge is formed between them. Such a bridge is always needed when two contours branch off from a single contour on an adjacent plane. The two contours are joined into one at the bridge in order to mesh them with the adjacent single contour. Ordinarily this is done at the closest approach between two contours, provided that other conditions are satisfied. This can be the wrong place if the actual branching opened a wider gap than some other close approach between the contours. Assign the same connection number to the two points that should be joined between the two contours. The midpoint of the line between the points must be located over the interior of the single contour on the adjacent plane. Be sure not to have any other matching connection numbers between those two contours. Be sure not to have the same point connection number in a contour on an adjacent plane, to avoid invoking any of the connection logic described above. If you use connection points in other ways, it is recommended that the connection points for bridging contours have distinctly higher numbers, such as 10. That way, if necessary, you can prevent the other points from being incorrectly used for bridges by setting the environment variable MIN_BRIDGE_CONNECT_NUM to a threshold value such as 10. Points below that threshold will be ignored when looking for bridge points.
  3. If contour properties are being shown, then connection numbers can be used to control whether contours on adjacent sections are meshed together by Imodmesh. To connect two contours that do not overlap, give them the same connection number. To prevent a connection between two contours that do overlap, give them two different connection numbers.
• General value: shows the value that has been stored, if any, for the current point or contour. These values can be inserted into a model with programs such as Imodcurvature, Patch2imod, Point2model, Imodfindbeads, Findbeads3d, and PEET.

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