In [1]:

    

import pymaid
import matplotlib.pyplot as plt

# Connect to CATMAID
rm = pymaid.CatmaidInstance('https://www.your.catmaid-server.org',
                            api_token='YOURTOKEN',
                            http_user='user', # omit if not required
                            http_password='pw') # omit if not required
# Get two neurons
nl = pymaid.get_neurons(['57311', '27295'])

# Plot using defaults
fig, ax = nl.plot2d()
plt.show()


    

In [2]:

    

fig, ax = pymaid.plot2d(nl)
plt.show()


    

In [3]:

    

fig, ax = pymaid.plot2d(nl,
                        color={'57311': 'k', '27295': 'y'},
                        connectors=False,
                        linewidth=1.5)
plt.show()


    

In [4]:

    

# Reverse order in CatmaidNeuronList
nl_rev = nl[::-1]
fig, ax = pymaid.plot2d(nl_rev,
                        color={'57311': 'k', '27295': 'y'},
                        connectors=False,
                        linewidth=1.5)
plt.show()


    

In [5]:

    

# Plot using matplotlib's 2.5D capabilities
fig, ax = nl.plot2d(method='3d',
                    connectors=False,
                    linewidth=1.5)

# Change from default frontal view to lateral view by changing the azimuth
ax.azim = 0

# Zoom in a bit
ax.dist = 6

plt.show()


    

In [6]:

    

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

# Change from default frontal view to top view by changing the elevation
ax.elev = 90

# Zoom in a bit
ax.dist = 6

plt.show()


    

In [7]:

    

fig, ax = nl.plot2d(method='3d_complex',
                    connectors=False,
                    linewidth=1.5)

for i in range(0,360,5):
   # Change rotation
   ax.azim = i
   # Save each incremental rotation as frame
   plt.savefig('_frames/frame_{0}.png'.format(i), dpi=200)
    
plt.clf()


    

    






<Figure size 432x432 with 0 Axes>

In [8]:

    

nl2 = pymaid.get_neurons('annotation:glomerulus DA1')

fig, ax = nl2.plot2d(method='3d_complex',
                     connectors=False,
                     linewidth=1.5)

ax.dist = 6

plt.show()


    

In [9]:

    

# Retrieve volume
lh = pymaid.get_volume('LH_R')

# Set color and alpha
lh.color = (0, 1, 0, .1)

# Plot
fig, ax = pymaid.plot2d([nl ,lh], method='3d_complex', linewidth=1.5, connectors=False)
ax.dist = 6

plt.show()


    

In [10]:

    

# Plot neurons first
fig, ax = nl.plot2d(method='3d_complex', linewidth=1.5, connectors=True)

# Add volume on existing ax
_ = pymaid.plot2d(lh, method='3d_complex', ax=ax)

ax.dist = 6

plt.show()