Tracing with the automatic mode(3D)
There are two ways to implement automatic tracing:
- For a tracing using the defaults, click the Trace button.
- For a more accurate or faster tracing, adjust the settings first, then click the Trace button. The settings give you the opportunity to review seed placement, which is used to initiate the automatic tracing.
To continue incomplete automatic tracings, you can use the user-guided tracing mode.
Getting ready to trace
- Open an image stack or single images.
- Make image adjustments as necessary.
- If you're using the 3D Volume view, select Partial projection under Image stack settings in the Image Display panel.
- Click the Vessel button to display the Trace Vessels panel and select Automatic.
- Select a tracing method.
Directional Kernels
With this method, four directional kernels are matched to the image data. For a given point within the vessel, the algorithm identifies the best positions and orientations for the top, bottom, left, and right kernels surrounding the point. The positions and orientations results are combined to estimate the next point to trace. Points are estimated until a set of stopping criteria is met.
For details on the algorithm, see Rapid automated three-dimensional tracing of neurons from confocal image stacks (Al-Kofahi, Lasek, Szarowski, Pace, Nagy, Turner, and Roysam, 2002).
Rayburst Crawl
The detection is implemented from a segment centerline to its outer edges (manuscript in preparation).
Voxel Scooping
This algorithm generates clusters of voxels iteratively along the vessel. These clusters are then used to position the nodes that define the centerline of the vessel.
For details on the algorithm, see Three-Dimensional Neuron Tracing by Voxel Scooping (Rodriguez, Ehlenberger, Hof, & Wearne, 2009).
If you trace automatically then decide to change the tracing method, click the Clear Tracing button first, then click Trace again.
Tracing after adjusting the settings
- Click Show settings.
- In the Display Seeds tab, click the Display Seeds button.
- Optional: To change the seed color, use the color picker next to the Hide Seeds button.
- To adjust the number of seeds, use the slider and the density buttons.
- Click the Refine Seeds tab.
- Click the validate Seeds button. The program applies an algorithm to evaluate seed placement.
- Optional: To decrease the number of unwanted seeds, increase the Refine filter value .
- Optional: Add or remove seeds manually.
- To add a seed, click in the image.
- To change the color of manually added seeds, use the color picker.
- Select the Remove radio button.
- Hover the mouse over a branch to see the circular cursor.
- Hold down CTRL and scroll the mouse wheel to resize the cursor.
- Click in the image to remove seeds within the cursor radius OR hold down CTRL and drag to remove contiguous seeds.
Adding seedsRemoving seeds - Click the Trace tab to modify the tracing settings.Settings
- Sensitivity: Use the slider or type a value to adjust sampling density.
- Gap tolerance: Use the slider to change the maximum acceptable distance between two segments to make a connection.
- Remove traces shorter than: Enter a value to ignore objects that may be mistaken for traces in a noisy image.
- Connect branch segments: Check to have the program connect branches according to the Branch Connections Criteria defined in the Advanced Settings (see details in Trace vessels (automatic) panel (3D)).
- Click the Trace button to start the automatic tracing.