Streamlines (ImageXd)

Streamline allows the tracking of channels or structures from a vector field (for example, from Diffusion). It creates streamlines based on seed points and a vector field.

You can found a Matlab implementation here:
Kupczik K, Stark H, Mundry R, Neininger F, Heidlauf T, Röhrle O (2015). Reconstruction of muscle fascicle architecture from iodine-enhanced microCT images: a combined texture mapping and streamline approach. Journal of Theoretical Biology 382 (7): 34–43. DOI:10.1016/j.jtbi.2015.06.034 / ISSN:0022-5193


In this example, we use a part of an image stack from Julian Sartori (Thanks for the support!), which shows the achilles tendon of a rat.

Download: Image stack

And the results from Diffusion.

Download: Vector stack
Download: Reduced vector stack


First step
Calculate the streamlines from the vector field.

→ ImageXd

vector.load "stack_vector.nii.gz"
vector.smooth 3

//vector.stream // calculate streamlines with steps 1 for all seed points
vector.stream.random 1000

line.save "stream.lines" // output for cloud2
line.save.trackvis "stream.trk" // output for the software Trackvis

vector.load "stack_reduce.nii.gz"

line.new
//vector.stream // calculate streamlines with steps 1 for all seed points
vector.stream.random 1000

line.save "stream_reduce.lines" // output for cloud2
line.save.trackvis "stream_reduce.trk" // output for the software Trackvis

// vector.stream.seeds := 1 // 0:all, 1(default):only at new points, 2:only at new points around -1..1, ...
// vector.stream.snakes := 0 // 0(default):all, 1:only for new points, 2:only for new points around -1..1, ...
// vector.stream.steps := 1 // streamlines with steps 1(default) (i.e. 0.5 or 2)
// vector.stream.angles := 0 // streamlines with segment angle 0°(default) (i.e. 5°, 10°)
// vector.stream.stop.angle := 180 // streamlines stops for wrong directions 180°(default) (i.e. 45°)
// vector.stream.stop.length := 0 // streamlines stops for too long streamlines (0(default)=diagonal of bounding box)

// vector.stream.nodes // calculate stream lines like vector.stream and increments corresponding scalar value

// vector.stream // calculate streamlines for all seed points from a vector field
// vector.stream.random 100 // calculate 100 streamlines
// Note: A zero point <0,0,0> calculates the center point of your stack!
// vector.stream.slice <10,10,10> <1,1,0> // calculate streamlines for all points on a plane (point*normal) from a vector field
// vector.stream.slicex 10 // calculate streamlines for all points on the x plane (value*<1,0,0>) from a vector field
// vector.stream.slicey 10 // calculate streamlines for all points on the y plane (value*<0,1,0>) from a vector field
// vector.stream.slicez 10 // calculate streamlines for all points on the z plane (value*<0,0,1>) from a vector field


Second step
Evaluation (with cloud2 please use *.lines).


stream.lines (x,y view)

stream_reduce.lines (x,y view)

stream.lines (y,z view)

stream_reduce.lines (y,z view)

→ Cloud2

calculate.fit.lines.degree 5 1


stack.lines (x,y view)

stack.lines (y,z view)