Figure for probeinterface paper¶

Here a notebook to reproduce figures for paper

ProbeInterface: a unified framework for probe handling in extracellular electrophysiology

In [2]:

from probeinterface import plotting, io, Probe, ProbeGroup, get_probe
from probeinterface.plotting import plot_probe_group

import numpy as np
import matplotlib.pyplot as plt

%matplotlib inline

In [3]:

# create contact positions
positions = np.zeros((32, 2))
positions[:, 0] = [0] * 8 + [50] * 8 + [200] * 8 + [250] * 8
positions[:, 1] = list(range(0, 400, 50)) * 4
# create an empty probe object with coordinates in um
probe0 = Probe(ndim=2, si_units='um')
# set contacts
probe0.set_contacts(positions=positions, shapes='circle',shape_params={'radius': 10})
# create probe shape (optional)
polygon = [(-20, 480), (-20, -30), (20, -110), (70, -30), (70, 450),
           (180, 450), (180, -30), (220, -110), (270, -30), (270, 480)]
probe0.set_planar_contour(polygon)

In [4]:

# duplicate the probe and move it horizontally
probe1 = probe0.copy()
# move probe by 600 um in x direction
probe1.move([600, 0])

# Create a probegroup
probegroup = ProbeGroup()
probegroup.add_probe(probe0)
probegroup.add_probe(probe1)

In [5]:

fig2, ax2 = plt.subplots(figsize=(10,7))
plot_probe_group(probegroup, ax=ax2)

In [6]:

fig2.savefig("fig2.pdf")

In [7]:

probe0 = get_probe('cambridgeneurotech', 'ASSY-156-P-1')
probe1 = get_probe('neuronexus', 'A1x32-Poly3-10mm-50-177')
probe1.move([1000, -100])

probegroup = ProbeGroup()
probegroup.add_probe(probe0)
probegroup.add_probe(probe1)

fig3, ax3 = plt.subplots(figsize=(10,7))
plot_probe_group(probegroup, ax=ax3)

In [8]:

fig3.savefig("fig3.pdf")

In [9]:

manufacturer = 'cambridgeneurotech'
probe_name = 'ASSY-156-P-1'

probe = get_probe(manufacturer, probe_name)
print(probe)

cambridgeneurotech - ASSY-156-P-1 - 64ch - 4shanks

In [10]:

probe.wiring_to_device('ASSY-156>RHD2164')

fig4, ax4 = plt.subplots(figsize=(12,7))
plotting.plot_probe(probe, with_device_index=True, with_contact_id=True, title=False, ax=ax4)
ax4.set_xlim(-100, 400)
ax4.set_ylim(-150, 100)

Out[10]:

(-150.0, 100.0)

In [11]:

fig4.savefig("fig4.pdf")

In [12]:

probe.device_channel_indices

Out[12]:

array([47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31,
       30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14,
       13, 12, 11, 10,  9,  8,  7,  6,  5,  4,  3,  2,  1,  0, 63, 62, 61,
       60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48])

In [13]:

probe.to_dataframe(complete=True)

Out[13]:

	x	y	contact_shapes	width	height	shank_ids	contact_ids	device_channel_indices	si_units	plane_axis_x_0	plane_axis_x_1	plane_axis_y_0	plane_axis_y_1
0	522.5	137.5	rect	11.0	15.0	2	1	47	um	1.0	0.0	0.0	1.0
1	500.0	50.0	rect	11.0	15.0	2	2	46	um	1.0	0.0	0.0	1.0
2	522.5	187.5	rect	11.0	15.0	2	3	45	um	1.0	0.0	0.0	1.0
3	500.0	125.0	rect	11.0	15.0	2	4	44	um	1.0	0.0	0.0	1.0
4	772.5	112.5	rect	11.0	15.0	3	5	43	um	1.0	0.0	0.0	1.0
...	...	...	...	...	...	...	...	...	...	...	...	...	...
59	772.5	37.5	rect	11.0	15.0	3	60	52	um	1.0	0.0	0.0	1.0
60	750.0	150.0	rect	11.0	15.0	3	61	51	um	1.0	0.0	0.0	1.0
61	750.0	50.0	rect	11.0	15.0	3	62	50	um	1.0	0.0	0.0	1.0
62	750.0	125.0	rect	11.0	15.0	3	63	49	um	1.0	0.0	0.0	1.0
63	772.5	12.5	rect	11.0	15.0	3	64	48	um	1.0	0.0	0.0	1.0

64 rows × 13 columns