In [1]:

    

import pymaid
import matplotlib.pyplot as plt

rm = pymaid.CatmaidInstance('server_url', 'api_token', 'http_user', 'http_password')

n = pymaid.get_neurons(16)

fig, ax = n.plot2d(connectors=False, linewidth=1.5)
plt.show()


    

In [2]:

    

# Resample to 10um
resampled = pymaid.resample_neuron(n, 10000)

# Downsample by factor 10
downsampled = pymaid.downsample_neuron(n, 10)


    

In [3]:

    

fig, axes = plt.subplots(1, 3, figsize=(18,5))

_ = pymaid.plot2d(n.nodes[['x', 'y', 'z']].values,
                  ax=axes[0])

_ = pymaid.plot2d(resampled.nodes[['x', 'y', 'z']].values,
                  ax=axes[1])

_ = pymaid.plot2d(downsampled.nodes[['x', 'y', 'z']].values,
                  ax=axes[2])

for ax, title in zip(axes, ['Original', 'Resampled to 10um', 'Downsampled 10x']):
    ax.set_title(title)
    ax.set_axis_off()

plt.show()


    

In [4]:

    

import pandas as pd

tn_id_comparison = pd.concat([n.nodes[['treenode_id']], resampled.nodes[['treenode_id']]], axis=1)
tn_id_comparison.columns = ['original IDs', 'after resampling']

tn_id_comparison.head()


    

    
Out[4]:







  

    

      

      
original IDs
      
after resampling
    
  
  

    

      
0
      
126378
      
126378.0
    
    

      
1
      
10344019
      
3194824.0
    
    

      
2
      
30307659
      
10341970.0
    
    

      
3
      
10343690
      
125420.0
    
    

      
4
      
30018122
      
10370725.0