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A 3D editing plugin
User: How to model 
- Step by step tutorial on SOLID OBJECTS.
- Fast tutorial on balls and pipes (for instance nuclei and axons).
Step by step tutorial on SOLID OBJECTS
2 - Make some groups at the "Set Groups" button. Be sure to name them with both a short and an informative name. Add also a color ranging from 0 to 255 to each group (gray scale). You can add groups later if necessary. Click "Apply changes and close".
3- Scroll the slice selector until a desired part of the object to model shows.
4- Choose a group from the groups pulldown menu (something like Group1(255).
5- Choose a tool at the pulldown menu that says "Bezier" by default. This tutorial will use the Bezier tool.
6- Click and drag at an edge of the area to outline. Move until the perimeter of the area shows an irregularity and click again. Adjust interpolation points as necessary to match the bezier curve with the perimeter of the area. Add as many points as necessary. You may delete points by control+click.
7- You may add points between two existing points by clicking on the bezier curve itself. Also, you can reset interpolation points by alt+drag on a point (not on a interpolation point).
8- Shift+click on a point to close the curve.
9- Click the "Add" button (or the A key).
10- Move on to next slice. You'll notice the curve is still on the screen. Adjust and add/delete points as to match the area showing now. Alternatively, you may erase this curve by clicking "Clear" and start over.
11- You may move the entire curve by alt+drag on the screen (not on a point or over the curve).
12- You may open the curve for better editing by shift+clicking on a point. Remember to close it again before adding the curve.
13- You may undo any step at any time by selecting it from the history list. You can set the number of history steps in the "Options" popup menu.
14- Push "Save P" anytime to save your work in a .shapes file. This can be opened again anytime by pushing "Open P".
15- Repeat previous steps until all slices where the object shows have a bezier curve (although it is not necessary that ALL have them; if a curve is missing in the middle, the program will work exactly the same, without z-axis being disturbed).
16- Make sure there aren't two curves belonging to the same group in the same slice. This would mess the 3D object. You may scroll fast to check this with the "<" and ">" shortcuts.
17- Push the "Save DXF" button and adjust options. Fundamental: DEPTH (slice separation in pixels). In a confocal stack, this information usually comes in the image file; click control+i to read file information. You may cap the object (add a surface at top and/or bottom) so that it looks solid.
18- Open the .dxf file in an application such as Blender (free at blender.org), Maya, AutoCAD or Amira. Experiment with the number of corners and skin method in the DXF popup dialog until your model looks best.
Fast tutorial on balls and pipes
1- Select ball tool and a group to assign them. Balls don't need to be grouped later, so more than one group of balls with the same name can be set in the same slice (although I recommend against).
2- Set the radius of the ball (in pixels). A ball can be deleted with control+click, so you may try a few radii until finding one that fits. Drag the ball around by click-drag on the center of it.
--->update 15 Jan 2005 : Hold shift to interactive modify the ball radius while click+drag the mouse. Works at making the ball and any time later on.
3- Add as many balls per slice, then click "Add". You may then change group and set a new field of balls in the same slice, or in any other.
4- As you scroll through slices, you'll notice balls of the current group in the previous slice are drawn in red, and in the next slice, in blue. This provides a guide for not repeating balls. Remember each ball (a circle on the screen) will be a sphere.
5- Adjust "ball meridians" and "ball parallels" in the DXF popup menu. The more there are, the better the sphere (and also the bigger the file).
PIPES:
1- Select pipe tool and a group. Pipes are not added to a slice since each node -each click- can lay on a different slice.
2- Set an appropiate radius for a pipe point. Every pipe point can have a different radius.
3- Add points by click-drag. Bezier curves are used; drag interpolation points to adjust the pipe. Alt+drag to reset interpolation points. Drag the point to, well, drag it around. --->update 14 Feb 2005 : Hold shift to interactive modify the point radius while click+drag the mouse. Works after making the point.
BE WARNED: if you don't extend the control points when adding a new point, i.e. adding a point by a click and not by a click-drag, the pipe will not be rendered appropiately in the DXF file, and the DXF file may be truncated due to problems with divisions by zero and so on. You can extend the control points anytime by alt+drag over a point.
4- As you scroll through slices, you'll notice pipe segments in current slice are white, red in previous and blue in next. This helps the user know the z-direction of the pipe.
5- "Add" pipe. Adjust "pipe parallels" in DXF popup menu to adjust the number of sides the pipe will have (it's a polygon). More sides means better roundness.