Visualization

Trace Visualization

brainlit.viz.skeletonize(img: np.ndarray, points: pd.DataFrame)

Draw lines between points that are connected to produce binary mask

Parameters

• {3d array} -- image (img) --

• {pandas dataframe} -- dataframe with swc points as output by combine_swc_img.points2voxel (points) --

Returns

[3d array] -- binary mask showing skeletonization between points

brainlit.viz.Bresenham3D(x1: int, y1: int, z1: int, x2: int, y2: int, z2: int)

Takes two coordinates and gives the set of coordinates that connects them with a straight line

Adapted from https://www.geeksforgeeks.org/bresenhams-algorithm-for-3-d-line-drawing/

Parameters

• {int} -- first x coodinate (x1) --

• {int} -- first y coodinate (y1) --

• {int} -- first z coodinate (z1) --

• {int} -- second x coodinate (x2) --

• {int} -- second y coodinate (y2) --

• {int} -- second z coodinate (z2) --

Returns

[list] -- list of x coordinate connecting the points [list] -- list of y coordinate connecting the points [list] -- list of z coordinate connecting the points