Notebook

In [1]:

import pymaid

# Connect to CATMAID
rm = pymaid.CatmaidInstance('https://www.your.catmaid-server.org',
                            'HTTP_USER' ,
                            'HTTP_PASSWORD',
                            'TOKEN')

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

In [2]:

# Generate a plotly figure
fig = nl.plot3d(backend='plotly', connectors=True, width=800)

In [3]:

# Import plotly bindings
import plotly.offline
plotly.offline.init_notebook_mode(connected=True)

# Generate the figure without plotting it right away
fig = nl.plot3d(backend='plotly', connectors=True, width=1200, plotly_inline=False)

# This will open the plot in a separate browser window
plotly.offline.plot(fig, filename='3d_plot.html')

In [4]:

# Provide colors
vols = [pymaid.get_volume('LH_R', color=(255, 0, 0, .2)),
        pymaid.get_volume('LH_L', color=(0, 255, 0, .2))]
fig = pymaid.plot3d([nl, *vols], backend='plotly', width=1200)

In [5]:

cust_vol = pymaid.Volume(vertices = [(1, 2, 1), (5, 6, 7), (8, 6, 4)],
                         faces = [(0, 1, 2)],
                         name = 'custom volume',
                         color = (255, 0, 0))
fig = pymaid.plot3d(cust_vol, backend='plotly', width=1200)

In [6]:

viewer = nl.plot3d()

In [7]:

viewer.screenshot('screenshot.png', alpha=True)

In [8]:

nl2 = pymaid.get_neurons([987675, 543210])
nl2.plot3d()

In [9]:

nl2.plot3d(clear3d=True)

In [10]:

pymaid.clear3d()

viewer.clear()

The viewer will survive simply closing the window. To wipe canvas from memory do:

In [11]:

pymaid.close3d() #or
viewer.close()

In [12]:

# Open two viewers
v1 = pymaid.Viewer()
v2 = pymaid.Viewer()

# Add neurons to each one separately
v1.add(nl)
v2.add(nl2)

# Clear one viewer
v1.clear()

# Close the second viewer
v2.close()