notebook.community

Edit and run



In [1]:

    
import pymaid
import matplotlib.pyplot as plt

# Connect to CATMAID
rm = pymaid.CatmaidInstance('www.your.catmaid-server.org',
                            'api_token' ,
                            'http_user',  # omit if not required
                            'http_password') # omit if not required

# Get some neurons
nl = pymaid.get_neurons(['57311', '27295'])



In [2]:

    
fig, ax = pymaid.plot2d(nl, method='2d',
                        connectors=False,
                        linewidth=1.5,
                        depth_coloring=True)

plt.show()



In [3]:

    
fig, ax = pymaid.plot2d(nl, method='3d',
                        connectors=False,
                        linewidth=1.5,
                        depth_coloring=True)

# Rotate to top view
ax.elev = 90

# Zoom in a bit
ax.dist = 6

plt.show()