Multi shank probes

This example shows how to deal with multi-shank probes.

In probeinterface this can be done with a Probe object, but internally each probe handles a shank_ids vector to carry information about which contacts belong to which shanks.

Optionally, a Probe object can be rendered split into Shank.

Import

import numpy as np
import matplotlib.pyplot as plt

from probeinterface import Probe, ProbeGroup
from probeinterface import generate_linear_probe, generate_multi_shank
from probeinterface import combine_probes
from probeinterface.plotting import plot_probe

Let’s use a generator to create a multi-shank probe:

multi_shank = generate_multi_shank(num_shank=3, num_columns=2, num_contact_per_column=6)
plot_probe(multi_shank)

(<matplotlib.collections.PolyCollection object at 0x7f6b982d9e10>, <matplotlib.collections.PolyCollection object at 0x7f6b98237d90>)

multi_shank is one probe object, but internally the Probe.shank_ids vector handles the shank ids.

print(multi_shank.shank_ids)

['0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1' '1' '1' '1' '1'
 '1' '1' '1' '1' '1' '1' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2']

The dataframe displays the shank_ids column:

df = multi_shank.to_dataframe()
df

	x	y	contact_shapes	radius	shank_ids	contact_ids
0	0.0	0.0	circle	6.0	0
1	0.0	20.0	circle	6.0	0
2	0.0	40.0	circle	6.0	0
3	0.0	60.0	circle	6.0	0
4	0.0	80.0	circle	6.0	0
5	0.0	100.0	circle	6.0	0
6	20.0	0.0	circle	6.0	0
7	20.0	20.0	circle	6.0	0
8	20.0	40.0	circle	6.0	0
9	20.0	60.0	circle	6.0	0
10	20.0	80.0	circle	6.0	0
11	20.0	100.0	circle	6.0	0
12	150.0	0.0	circle	6.0	1
13	150.0	20.0	circle	6.0	1
14	150.0	40.0	circle	6.0	1
15	150.0	60.0	circle	6.0	1
16	150.0	80.0	circle	6.0	1
17	150.0	100.0	circle	6.0	1
18	170.0	0.0	circle	6.0	1
19	170.0	20.0	circle	6.0	1
20	170.0	40.0	circle	6.0	1
21	170.0	60.0	circle	6.0	1
22	170.0	80.0	circle	6.0	1
23	170.0	100.0	circle	6.0	1
24	300.0	0.0	circle	6.0	2
25	300.0	20.0	circle	6.0	2
26	300.0	40.0	circle	6.0	2
27	300.0	60.0	circle	6.0	2
28	300.0	80.0	circle	6.0	2
29	300.0	100.0	circle	6.0	2
30	320.0	0.0	circle	6.0	2
31	320.0	20.0	circle	6.0	2
32	320.0	40.0	circle	6.0	2
33	320.0	60.0	circle	6.0	2
34	320.0	80.0	circle	6.0	2
35	320.0	100.0	circle	6.0	2

We can iterate over a multi-shank probe and get Shank objects. A Shank is linked to a Probe object and can also retrieve positions, contact shapes, etc.:

for i, shank in enumerate(multi_shank.get_shanks()):
    print('shank', i)
    print(shank.__class__)
    print(shank.get_contact_count())
    print(shank.contact_positions.shape)

shank 0
<class 'probeinterface.shank.Shank'>
12
(12, 2)
shank 1
<class 'probeinterface.shank.Shank'>
12
(12, 2)
shank 2
<class 'probeinterface.shank.Shank'>
12
(12, 2)

Another option to create multi-shank probes is to create several Shank objects as separate probes and then combine them into a single Probe object

# generate a 2 shanks linear
probe0 = generate_linear_probe(num_elec=16, ypitch=20,
                               contact_shapes='square',
                               contact_shape_params={'width': 12})
probe1 = probe0.copy()
probe1.move([100, 0])

multi_shank = combine_probes([probe0, probe1])

print(multi_shank.shank_ids)

['0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1'
 '1' '1' '1' '1' '1' '1' '1' '1' '1' '1' '1' '1' '1' '1']

plot_probe(multi_shank)

plt.show()