Dendrometer User's Guide

For Dendrometer Version 0.8

Menus

Tracing Window

The main (or "tracing") window is where your volume is displayed for tracing of the dendrites. It is divided into four subpanes. The largest is the X-Y view at lower right; this displays on Z-slice of your image stack at a time. In other words, this pane displays a single image from the stack of images. Above and to the left of this pane are the X-Z and Z-Y views, respectively. These are cross-sections of your volume perpendicular to the X-Y plane, and arranged so that each shares one axis with the X-Y view. This is the classic "blueprint" arrangement. It results in an unused area at the upper left which can be ignored.

For all three views, the slice displayed is the one that corresponds to the cursor position. The cursor is a crosshairs shown in all three views. It is moved by clicking the mouse in any of the three. When the X position of the cursor changes, a different slice will be displayed in the Y-Z view. When the Y position is changed, a new X-Z view is displayed; and when the Z position is changed, the main (X-Y) subpane is updated. You can quickly explore your volume in this way.

You may also nudge the cursor using the keyboard. The arrow keys move the cursor in X and Y, as do the numbers 4, 6, 8, and 2 on the numeric keypad; - and + (minus and plus) move the cursor in Z.

To place a node, first move the cursor to the center of the node. Check all three views to make sure you've centered it in all three dimensions. Then hold the shift key, click again, and drag the circle so that it just fills the dendrite in three dimensions. (Actually, the node is a sphere; thus it appears round in all three views.) Unless it is the first node you've placed, it will be connected to the previously selected node. The new node will become the currently selected node, ready to be connected to the next. If you need to adjust the node diameter, hold the shift key and use the arrow keys (or the numeric keypad).

To select an existing node, just click near its center. Remember that this may take two clicks, since you have to properly locate it in three dimensions. The selected node is shown in green, whereas all other nodes are red. As described above, the currently selected node will be connected to any newly created node. You can also delete this node by pressing the [delete] or [del] key.

To move the currently selected node, hold the option key, grab the node with the mouse, and drag it to a new position. You may also hold the option key down, and nudge the node with the arrow keys or numeric keypad.

Rendering Window

The rendering window displays the skeleton of your traced structure in a spinning 3-dimensional box. The trace lines are black, while the box frame is blue, to somewhat blend into the white background. (Note that the bounding box is purposely inset by 20 pixels in X and Y, so you may have some branches that stick out of the box somewhat.)

At the top of the window are rotation speed controls and indicators, one each for the X, Y, and Z axes. Red meters between each set of buttons indicate the speed and direction of rotation around that axis. By clicking the left and right buttons, you can change the speed. You can also stop rotation on an axis by clicking between the buttons (i.e., on the label or on the speed indicator).

You can leave the rotation window up and spinning while you return to the tracing window for more work. It will continue to spin, though there may be pauses while the application is processing more important work. Changes in the tracings will be reflected immediately if the rendering is spinning in at least one axis.

http://www.strout.net/dendrometer/doc.html
Last Updated: 3/25/97 . . . . . . Joe Strout