Hyperstack

A hyperstack is a series of 3D image volumes (stacks) where each stack in the series is a sequential timepoint of the same volume. Taken together the Hyperstack interface is very flexible. This flexibility allows for different scoring strategies.

The overall goal is to:

  1. Score nodes, edges and slabs within each stack/timepoint using the Hyperstack Stack.
  2. Connect nodes between stacks/timepoints using Find Points.
  3. Connect edges between stacks/timepoints using Find Points.
  4. Browse your hyperstack and check all your work (done in 1-3) using a combination of all the interface elements.

1. Score nodes, edges and slabs within each stack/timepoint

From the main Hyperstack window, open a hyperstack stack for a given timepoint by entering the time point and pressing the ‘Hyperstack’ button. Annotate the stack with nodes, edges and slabs. Please see Hyperstack Stack more information.

2. Connect nodes between stacks/timepoints

Use the Find Points interface to specify nodes that go from one stack/timepoint to the next. The Find Points interface will generate fairly reliable guesses for the connection/correspondence of each  node across multiple stacks/timepoints.

3. Connect edges between stacks/timepoints

Again, use the Find Points interface to check and edit the connections of edges between stacks/timepoints.

Note: Once nodes are correctly connected between stacks/timepoints using Find Points, edges are easy to connect because each edge is associated with just two unique nodes. Assuming all the nodes and their corresponce between stacks/timepoints is specified correctly (step 2), the correspondence between edges can almost be done automatically.

4. Browsing a hyperstack

Once nodes are connected across stacks/timepoints, you can use the Hyperstack Map to visualize and browse all the nodes and their connections in the entire hyperstack.

 

Workflow [depreciated]

1) Find a branch-point to mark through a sequence of timepoints.

2) Start a new run by clicking ‘New Run’ button.

3) The next time you click, this will create a branchpoint where you clicked and proceed to the next timepoint.

Note. As you create a run, feel free to navigate around the stack: scroll up/down with the mouse-wheel and pan and zoom with arrow keys and +/-. You cn also go back to the previous timepoint or ahead to the next to get your bearings.

4) If you get through all the timepoints you are done with the run.

5) At a given timepoint you can decide to finish the run. Click ‘Finish Run’ and select an option:

  • Too Dim
  • Out of View
  • Subtraction

Note. IF you don’t like the placement of one of your branch points you can ‘Move’ the point by right clicking the point and selecting ‘Move Pnt’. You then drag the point around to the desired position and click somewhere away form the point to accept the new position.

Note. Once you are done with a run or if you make a mistake you can delete a point by right-clicking and selecting ‘Delete Pnt’. You can only delete points at the end of a run. To delete an entire run, start at the end and work backwards.

Note. If you Finish a run but decide later to continue it, you can select the point and select ‘Continue Run From Pnt‘.

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