In [1]:

    

import pymaid
import matplotlib.pyplot as plt

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

# Get a neuron
n = pymaid.get_neurons(16)


    

In [2]:

    

lh = pymaid.get_volume('LH_R')

in_lh = n.connectors[pymaid.in_volume(n.connectors, lh)]
in_lh.head()


    

    
Out[2]:







  

    

      

      
treenode_id
      
connector_id
      
relation
      
x
      
y
      
z
    
  
  

    

      
340
      
5464238
      
5464237
      
0
      
343524
      
160024
      
188200
    
    

      
341
      
10369976
      
10370122
      
1
      
383883
      
147184
      
177600
    
    

      
368
      
20452694
      
11296577
      
1
      
335499
      
154147
      
188280
    
    

      
369
      
20452694
      
20452710
      
1
      
336487
      
153234
      
188280
    
    

      
390
      
10736254
      
10736250
      
0
      
385618
      
136047
      
172120
    
  

In [3]:

    

fig, ax = pymaid.plot2d(n, connectors=True,
                        linewidth=1.5, method='3d',
                        cn_size=2)

cn_coords = in_lh[['x','y','z']].values

fig,ax = pymaid.plot2d(cn_coords, method='3d', ax=ax,
                       scatter_kws={'s': 20,
                                    'color': 'g',
                                    'marker': 'D'
                                   })

ax.dist = 5

plt.show()


    

In [4]:

    

# Import plotly bindings
import plotly.offline

# Initialize notebook mode
plotly.offline.init_notebook_mode(connected=True)


    

In [5]:

    

# Generate a plotly figure
fig = pymaid.plot3d([cn_coords, n] ,backend='plotly',
                    connectors=True, width=800,
                    scatter_kws={'color': (0,255,0), 'opacity': .5})

plotly.offline.iplot(fig)


    

    




WARNING : Looks like RGB values are 0-1. Converting to 0-255. (pymaid)
INFO  : Use plotly.offline.plot(fig, filename="3d_plot.html") to plot. Optimised for Google Chrome. (pymaid)