Hyperstack Stack



A Hyperstack inherits the majority of its functionality from stack.

Top control  bar

Contrast sliders and values. Set the lower and upper contrast values. Try them out.

Capture Pivot. Captures the selected node as a Pivot point. Pivot points are used to align stacks across timepoints. The X/Y position of the current pivot is the blue square.

Top/Bottom. Set the current contrast for the Top of the stack and the bottom of the stack. Turn this on and the contrast will be linearly adjusted between the top and bottom. This is useful if your stacks get dark towards the bottom.

Capture Contrast. Capture the current contrast settings


Shift + Click. Creates a new node. A node is usually a branch point of tubes.

N + Click. Connect two nodes with a new tube. Select the source node and then N+Click on the destination node to create a new tube.

S + Click. Create a slab along  a tube. The order of slabs along a tube goes from the Red node to Green node.

Esc. Cancel the current selection.

Visualizing Annotations

  • Nodes : Red points
  • Tubes : Red lines
  • Slabs : Blue points


Once a stack is annotated with node, edge and slab objects, clicking on an object will select it.

Use the point Info window (shift+?) to enter a text note for a node.

Select a slab to edit its radius with the Slab Radius Panel. Each slab has a line that is orthogonal (perpendicular) to the direction of the tube. The intensity profile along this line is analyzed to estimate the tube diameter at each slab.


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