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Tracing Dendrites

NeuronStudio automatically traces all connected dendrites of the neuron starting from a seed location you provide. Disconnected dendritic segments can be traced one at a time by re-positioning the seed location each time.

To start tracing a segment, select the seed tool Seed Tool from the tools panel or select Edit >> Mode >> Seed from the main menu. Then click on a projection over the segment to be traced.

TIP: Pressing the E key will switch to the seed mode as well.

NeuronStudio automatically determines the 3rd component of the seed location. For example if the current view is in the forward (XY) direction, the X and Y coordinates of the seed location are set by the mouse and the program proceeds to analyze the data in order to determine the appropriate Z coordinate for the seed based on intensity. After this is completed you may want to verify that the 3rd coordinate has been correctly set by looking at the other projections. The current seed location is only displayed when the seed tool is active, unless the View >> Seed Always Visible option has been selected in the main menu.

If the slice viewer is active, setting the seed while viewing from the forward (along the optical axis) direction will force the Z coordinate of the seed to be placed at the Z position of the current slice.

Setting a Seed

The next step is to initiate the actual tracing from the seed location. Select Run >> Build Neurites from the menu, or press the N key. NeuronStudio will show real-time animation of the tracing which you can use to monitor progress. A progress window will appear at the top of the display window. Hitting the cancel button on this progress window will terminate the tracing. All dendrites traced during this invocation of the procedure will be cleared, but previously traced dendrites will remain.

All detected dendrites will be traced along all possible paths. The tracing will be terminated though along a path that exits the boundaries of the region of interest (ROI) or dataset.

Automatic Tracing

After the tracing is complete, various post-processing filters are run and the final resulting model displayed.

TIP: Adjust the neurites settings to control the removal of unwanted small branches during the filtering process.

Model Filtering

You may also use this tool in the 3D window. Simply hover the mouse cursor over the place in the volume rendering where you would like to seed from and click. The program will try to center this seed automatically for you. The volume rendering must have been generated for this to work in the 3D window.

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