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Branch Order and Section Labels

Automated Branch Order

NeuronStudio provides the ability to classify the medial axis into branch orders. Orders are similar to sections in that they represent an (unbranching) sequence of points, but our definition allows it to cross through a junction point. The first is a centripetal labeling scheme where the lowest order is at the tips of the dendritic structure, with order increasing inwards towards the soma. In the figures below it can be seen that the order is increased only when 2 (or more) child branches with the same order intersect at a junction point. Centripetal ordering can be set for the current model by selecting the menu item Run >> Edge Labeling >> Centripetal Order.

The second is a centfrifugal labeling scheme where the lowest order is at the branches starting at the soma, with order increasing outwards. Whenever a branching point is encountered, the order is increased. Centrifugal ordering can be set for the current model by selecting the menu item Run >> Edge Labeling >> Centrifugal Order.

Closeup Centripetal Branch Order Complete Centripetal Branch Order Closeup Centrifugal Branch Order Complete Centrifugal Branch Order
Closeup view of the centripetal labeling scheme. Highest orders are near the soma. Order increases when 2 or more branches of the same order intersect at a branching point. Complete centripetal labeling of a cell. Closeup view of the centrifugal labeling scheme. Lowest orders near the soma. Order increases by 1 at each branchpoint. Complete centrifugal labeling of a cell.

Automated Section Labels

A section of a model can be defined as an unbranching set of medial axis points. Using NeuronStudio these can be color coded for easy visualization. In addition, these sections are given an integer index value that is used in the output of detected spines so that statistics such as spine density, etc., can be more easily calculated.

These sections also correspond to the definition of a section in compartmental modeling packages such as NEURON, and associated HOC files. The model can be exported into this format using NeuronStudio. In the outputted file a an array of sections is created, connected, and filled with 3D points. The figures below show the color-coded sections of some dendrites of a model. Note how each unbranching section is labeled in a different color.

Section labeling can be automatically set by the menu item Run >> Edge Labeling >> Depth First Sections or Run >> Edge Labeling >> Breadth First Sections.

Closeup Section Labeling Complete Section Labeling
Closeup view of the section labeling procedure. The branch points (or soma) delimit the start of the sections. Complete section labeling of a cell.

Manual Branch Order

To manually assign the branch order of any dendritic segment, first select its nodes using any of the neurite selection methods or advanced selection methods. Then use the Edit >> Set Order of Selected Neurites command from the main menu or right-click on the viewport using the neurite tool Neurite Tool and choose Set Order from the context menu. See also Labeling the Model for an image showing this context menu. This will bring up a dialog box as shown below. Then, just type the desired order number for the branch and hit OK to set the order or Cancel to abort.

Set Order Window

TIP: Currently the Propagate checkbox is not used.

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Send questions or comments to: alfredo.rodriguez@mssm.edu