Matplotlib: Annotating a 3D scatter plot

Maybe easier via ax.text(...):

from matplotlib import pyplot
from mpl_toolkits.mplot3d import Axes3D
from numpy.random import rand
from pylab import figure

 
m=rand(3,3) # m is an array of (x,y,z) coordinate triplets
 
fig = figure()
ax = fig.add_subplot(projection='3d')

for i in range(len(m)): #plot each point + it's index as text above
    ax.scatter(m[i,0],m[i,1],m[i,2],color='b') 
    ax.text(m[i,0],m[i,1],m[i,2],  '%s' % (str(i)), size=20, zorder=1,  
    color='k') 

ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
pyplot.show()

Calculate the 2D position of the point, and use it create the annotation. If you need interactive with the figure, you can recalculate the location when mouse released.

import pylab
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d import proj3d
fig = pylab.figure()
ax = fig.add_subplot(111, projection = '3d')
x = y = z = [1, 2, 3]
sc = ax.scatter(x,y,z)
# now try to get the display coordinates of the first point

x2, y2, _ = proj3d.proj_transform(1,1,1, ax.get_proj())

label = pylab.annotate(
    "this", 
    xy = (x2, y2), xytext = (-20, 20),
    textcoords = 'offset points', ha = 'right', va = 'bottom',
    bbox = dict(boxstyle = 'round,pad=0.5', fc = 'yellow', alpha = 0.5),
    arrowprops = dict(arrowstyle = '->', connectionstyle = 'arc3,rad=0'))

def update_position(e):
    x2, y2, _ = proj3d.proj_transform(1,1,1, ax.get_proj())
    label.xy = x2,y2
    label.update_positions(fig.canvas.renderer)
    fig.canvas.draw()
fig.canvas.mpl_connect('button_release_event', update_position)
pylab.show()