Hyperstack Find Points

Find Points is an interface to connect both nodes and tubes between two stacks (between timepoints). In both cases, an automatic Guess is generated and the user can (i) accept the guess or (ii) specify the connection manually.

For nodes, the automatic guess uses the Pivot Point, for edges the automatic guess uses the two nodes that make up the edge. Using a Pivot Point, the automatic guess can be correct >90% of the time.

Nodes

findpnts_nodes2

Here the Find Points interface is being used to connect nodes between timepoint 9 and timepoint 10. Each node in the first timepoint has a row in the list. In this example, the 17th node is selected and is shown in the two image stacks (purple triangle).

The blue colored selection indicates the current pivot point. It is shown in the list and in the two image stacks.

For each source node in the first time point (src) there is a guess telling us the node it potentially matches in the second timepoint (Guess).  The goal here is to fill in the proper connection/correspondence  by filling in the proper destination node (Dst). In most cases, when the guess is correct this is done by simply copying the Guess to the Dst. If the Guess is not correct, the user selects the proper destination node (in the second timepoint) and using a right-click selects ‘Connect Nodes’.

Reverse Lookup. If a node in the second timepoint (timepoint 10 in this exmaple) does not have a match in the first timepoint (timepoint 9 in this example) it is appended to the end of the list. This node can be selected as usual and allows for a reverse lookup.

Tubes

findpnts_tubes2

Here the Find Points interface is being used to connect edges from time point 9 to timepoint 10. Edge #20 is selected in the list and is displayed in the two image stacks (purple line). In comparison to connecting nodes, connecting edges depends on the source (red) and destination (green) node of each edge. If all nodes have have been correctly matched using the Find Points interface, the edges will also be matched and there is no need for editing.

Important Concepts

Pivot Point. For each source node we generate a guess node using a pivot point in the two images. A pivot point is a special node that the user identifies as being the same in both images. By using the 3D position of this pivot, we can search from the source image to the destination image and look for nodes near that pivit (these become the Guess). This allows for the registration of your image stacks to be fairly innacurate. This begins to fail if the density of the nodes is high, we have trouble deciding who is actually the connecting node.

Only one edge between two nodes. Each edge connects two nodes. We do not allow two edges between the same two nodes (anastomosis). While this occasionally happens in vascular tubes, it is very uncommon. When this does occur we simply flag one or both of the nodes that have a double edge with a text note so we can return to this special case in the future.

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