segmenting-1d-tracks.md

Segmenting 1D tracks

To segment a 1D track, such as a fibre track, or a silicone probe track, select the Track tracing button in the Segmentation panel.

{% hint style="info" %} For more information about how to process silicon probe tracks, please see Silicon probe tracking. {% endhint %}

Then:

• Click the Add track button
• If required, rename the track (by selecting the track_0 text)
• Navigate to where you want to draw your region of interest.
• Make sure the add points mode is activated (by selecting the + symbol)
• Trace your track by adding points along it. You can add as many, or as few as you like, and this can be done in 3D by changing the viewer plane as you go along.

{% hint style="info" %} Make sure you select the points in the order you wish them to be joined {% endhint %}

• Repeat the above for each track you wish to trace
• If the brain surface is damaged, you may not be able to trace perfectly from the surface. If you want to add an additional first point at the surface of the brain, click Add surface points. Selecting this option will add an additional point at the closest part of the brain surface to the first point, so that the track starts there.
• The points can then be joined using spline interpolation by clicking Trace tracks. You can change:
  • Fit degree- what order spline fit to use (the default is 3, cubic)
  • Spline smoothing - how closely or not to fit the points (lower numbers fit more closely, for a less smooth interpolation)
  • Spline points - this doesn't affect the interpolation, but determines how many points are sampled from the interpolation (used for the summary)
  • Summarise- defaults to on, this will save a csv file, showing the brain area for each part of the interpolated track (determined by Spline points )
  • Add surface point If the brain surface is damaged, you may not be able to trace perfectly from the surface. Selecting this option will add an additional point at the closest part of the brain surface to the first point, so that the track starts there.

You will then see a the track fit appear in the napari window, and a .csv file will be saved, showing the brain region for every spline point along the track.

You can also use Save to save your points to be reloaded at a later date, and if you loaded your data in atlas space, you can also export the track to brainrender. The file will be saved as e.g. track_0.npy. If you're using the brainrender GUI, use the Load cells button to load the track. Alternatively, using the Python API, you can visualise the track as follows:\

from brainrender import Scene
from brainrender.actors import Points
from myterial import blue

file = ("/path/to/track_0.npy")

scene = Scene()
scene.add(Points(file, colors=blue, radius=100, alpha=0.7))
scene.render()

{% hint style="info" %} All data will be saved into your brainreg output directory {% endhint %}