Segmenting 1D tracks#
For more information about how to process silicon probe tracks, please see Silicon probe tracking.
To segment a 1D track, such as a fibre track, or a silicone probe track, select the
Track tracing button in the
If required, rename the track (by selecting the
Navigate to where you want to draw your region of interest.
Make sure the add points mode is activated (by selecting the
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.
Make sure you select the points in the order you wish them to be joined
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:
Summarise- Defaults to on, this will save a csv file, showing the brain area for each part of the interpolated track (determined by
Save tracing- Defaults to off. This will save your segmentation layer at the same time as running the analysis (this may make your analysis take longer)
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)
Add surface points- 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 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 independently of the analysis 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. 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()
All data will be saved into your brainreg output directory
For more information about how to use automated methods to segment your feature of interest, please see Analysing segmentation from other napari plugins.